Cannabis Plant Anatomy: Get To Know Your Plant

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Added 15 May 2023

Every cannabis grower starts with little knowledge. 

But then, you want to learn more and more about your favorite plant and begin visiting forums, talking to friends, reading books, etc. 

However, there may be a lot of terms you don’t understand at all. For example, it’s important to look at the pistils of the cannabis plant before you harvest the buds, says a popular book, but what in the world are pistils? Are they similar to trichomes?

If you’ve just started growing cannabis, you may get confused very quickly. Although it’s not necessary to know everything about the plant, it will help a great deal to understand the fundamentals. You don’t need to become a mad scientist, but just becoming familiar with the basics will make your life easier. 

Also, if these terms intimidate you, know that you’re not alone. Not everyone is an expert biologist, and there’s no shame in learning. You just have to start somewhere. But, one day, you’ll know the plant so much that these exotic terms may not sound so scary anymore. 

So, here’s a basic anatomy of the cannabis plant you should know, whether you’re a hobbyist or a commercial grower. We will start from the bottom all the way to the top. 

1. Root System

Root System

Cannabis roots are vital for the plant's survival, as they anchor the plant to the soil, absorb nutrients and water, and store carbohydrates. In addition, the root system plays a crucial role in the plant's ability to absorb oxygen, which is necessary for healthy growth. Healthy roots equate to a healthy plant. 

Often, you’ll see that the plant struggles to survive if the root system isn’t healthy. Hydroponic growers, in particular, are very careful to maintain the health of the roots since they are always in the water. Typically, healthy roots are white. In contrast, unhealthy roots may turn brown and slimy.  

Once the seed germinates, the story of the cannabis plant begins with a tap root. The tap root is the primary root that grows vertically into the soil. It develops from the radicle or the embryonic root that emerges from the seed. As the thickest and longest root of the cannabis plant that forms at the very beginning, the taproot forms the main root system. It provides stability to the plant and anchors it to the soil.

As the taproot grows, it absorbs nutrients plus water from the soil and stores nutrients. Later, the taproot develops lateral roots that spread out from the main stem. 

The taproot grows vertically downward, while the lateral roots grow horizontally and spread out in all directions. In short, once the taproot spreads itself, it develops fibrous roots that form a stable network of roots that spread in the soil. The fibrous roots are responsible for absorbing nutrients from the soil. They have a large surface area and are well adapted to uptake nutrition efficiently.

As the plant picks up speed and grows further, adventitious roots develop on the plant stems. You may have noticed these roots at times. Adventitious roots are the roots that develop from the stem or other parts of the plant other than the radicle. They may develop from the plant’s nodes, stems, or leaves. Typically, they form in response to stress, such as drought or injury, overwatering, nutrient deficiencies, or pest infestations, and they help the plant survive. They also help with cloning. 

The root system also contains the root crown — the part where the stem and roots meet, located just above the soil line. It is also sometimes called the root collar or the stem base. The root crown is an important part of the plant, as it serves as the connection point between the roots and the stem, and it also contains specialized cells involved in the growth and development of the plant.

One of the main purposes of the root crown is to provide stability and support for the cannabis plant. The roots of the plant anchor it firmly in the soil, while the stem provides structure and holds the leaves and flowers upright. The root crown acts as a transition zone between the two, and it plays a critical role in distributing nutrients and water throughout the plant.

The root crown also contains specialized cells called meristematic cells, which are responsible for the growth and development of new tissue. These cells divide rapidly, creating new cells that can differentiate into different types of tissue, such as stem, root, or leaf tissue. This allows the plant to grow and develop in response to environmental cues, such as light, water, and nutrient availability.

Another important function of the root crown is to protect the plant from damage and disease. The root crown is covered by a layer of tissue called the periderm, which helps to prevent pathogens and pests from entering the plant. The periderm also regulates the exchange of gases between the plant and the environment, and it plays a role in storing nutrients and carbohydrates.

2. Leaves


As soon as the seed germinates, you’ll see two tiny leaves emerging in all their glory. These leaves are called cotyledons. As embryonic leaves that are essential for the plant's early growth and development, the cotyledons kickstart the plant’s growth and let it survive for at least a couple of weeks. Cannabis plants typically have two cotyledons, also known as seed leaves, and serve several functions for the cannabis plant, including:

Nutrient storage

The cotyledons contain stored nutrients, such as carbohydrates, proteins, and lipids, that the plant uses for energy during its early stages of growth. These nutrients are transported from the endosperm to the cotyledons before germination, and the cotyledons serve as a source of energy for the developing plant until it can establish a functional root system and begin photosynthesis.


The cotyledons also perform photosynthesis, which is the process by which plants produce energy from sunlight. The cotyledons contain chloroplasts (you may have heard about them in school) which are the organelles responsible for photosynthesis, and they can produce energy using light even before the plant's true leaves emerge.


The cotyledons provide protection to the young plant by covering and enclosing the delicate apical meristem, which is the growing point of the plant. The cotyledons also shield the plant from environmental stress, such as high temperatures, low humidity, or excess light.

As the plant grows, the cotyledons will eventually die off and be replaced by the plant's true leaves. However, the cotyledons play a critical role in the plant's early growth and development, and their proper formation and function are essential for the survival of the plant.

In short, cotyledons of a cannabis plant are the first leaves that emerge from the seed after germination. They serve as a source of stored nutrients, perform photosynthesis, protect the young plant, and regulate plant hormones. 

True Leaves

After the emergence of the cotyledons, cannabis plants develop their true leaves, which are the leaves that will continue to grow and function throughout the plant's life cycle. The development of leaves in cannabis plants follows a specific pattern, with the plant producing one or two sets of leaves per week during the vegetative growth stage.

The first set of true leaves will typically have a single blade, while subsequent sets will have two blades, and so on. Each set of leaves will be larger and more complex than the previous set, and the plant will continue to produce new leaves until it reaches maturity.

Like the cotyledons, the leaves of the cannabis plant are the primary site of photosynthesis, where the plant converts light energy into chemical energy. The shape and size of the leaves vary depending on the strain of cannabis.

The anatomy of cannabis leaves can be divided into three main parts: the blade, the petiole, and the stipules.


The blade is the large, flat portion of the leaf that is responsible for most of the plant's photosynthesis. It consists of two main layers: the upper epidermis and the lower epidermis. The upper epidermis is covered in a waxy layer called the cuticle, which helps to prevent water loss from the leaf. The lower epidermis contains small pores called stomata, which allow for gas exchange and transpiration. Between the two layers of the epidermis is the mesophyll, which contains chloroplasts and is responsible for photosynthesis.


The petiole is the stalk that attaches the blade to the stem of the plant. It supports the weight of the leaf and transports nutrients and water to and from the blade. The petiole also contains vascular tissue, including the xylem and phloem, which help to transport water, nutrients, and sugars throughout the plant.


Stipules are small, leaf-like structures that grow at the base of the petiole. They are not always present on cannabis leaves, and when they are, they are often small and inconspicuous. Stipules are believed to play a role in protecting the young leaf bud as it develops.

In addition to these main parts, cannabis leaves also contain several other structures, such as trichomes, which are small, hair-like structures that grow on the surface of the leaf. Trichomes produce resin that contains cannabinoids and terpenes, which give the plant its unique scent and psychoactive effects. Trichomes can also protect the plant from predators and environmental stressors.

The leaves themselves comprise several layers, including the outermost layer, the epidermis, which is covered in trichomes. The leaves help the plant by aiding in several important processes, including photosynthesis, hormone regulation, and transpiration. 

Beneath the epidermis is the mesophyll, which is where chloroplasts are located, responsible for the photosynthesis process. Thanks to chlorophyll, the pigment that captures light energy, the leaves produce food for the plant. 

The stomata are small openings on the underside of the leaf that allow for gas exchange, which is necessary for the plant to take in carbon dioxide and release oxygen. 

Next, they aid with transpiration and regulate the plant's water balance by allowing water vapor to escape through the stomata. This helps prevent the plant from losing too much water through its leaves.

Finally, the leaves produce and regulate plant hormones, which are critical for the plant's growth and development. For example, auxins are responsible for initiating the growth of new leaves and branches, while cytokinins are involved in cell division and differentiation. You may already know about auxins as you train the plant. For instance, when you train the plant through LST, you force it to open up its canopy and redistribute the auxins to other parts of the plant, thereby triggering faster growth. 

As a cannabis grower, you may already know about fan leaves and sugar leaves. Let’s understand a bit more about them. 

Fan leaves and sugar leaves are two types of cannabis leaves that are differentiated by their appearance and their functions.

Fan Leaves

Fan leaves are large, flat leaves that grow at the top of the stem and branches of the cannabis plant. They are called "fan leaves" because they resemble the shape of a fan. Fan leaves play a key role in most of the plant's photosynthesis and transpiration. They are also a good indicator of the plant's overall health, as their appearance can reveal any nutrient deficiencies or other problems that the plant may be experiencing.

Sugar Leaves

Sugar leaves are smaller leaves that grow in and around the buds of the cannabis plant. They are called "sugar leaves" because they are covered in trichomes, which are small, hair-like structures that contain cannabinoids and terpenes. Sugar leaves are often used to make concentrates and extracts, as they are rich in resin and can be easily harvested and processed.

While fan leaves and sugar leaves serve different functions, they are both important for the growth and development of the cannabis plant.

3. Stem

Cannabis Stem

The stem of the cannabis plant is the plant's central support structure, transporting nutrition and water from the roots to the rest of the plant. The stem also has several layers, including the outermost layer, the epidermis, which is covered with tiny hairs called trichomes. 

Beneath the epidermis is the cortex, which is a layer of tissues. It stores water, carbohydrates, and nutrients that the plant uses for growth and reproduction. In addition, it contains the majority of the stem's cells and provides structural support to the plant.

The innermost layer is the pith, which contains soft, spongy tissue that stores water. It provides structural support to the stem and also stores carbohydrates.

Cannabis stems, or stalks, get their strength from the organization of the cells within the cortex. This arrangement creates a strong and flexible stem that can support the weight of the plant and withstand environmental stresses such as wind and rain.

4. Flowers/Buds

Cannabis buds

The flowers, also known as buds, are the reproductive organs of the cannabis plant. The female flowers contain the highest concentration of cannabinoids, which are the compounds responsible for the plant's psychoactive effects. In other words, that’s how you get high!

The buds comprise several parts, including the calyx, pistil, and trichomes. It is covered in trichomes, which contain the highest concentration of cannabinoids. The pistil is the female reproductive organ that collects pollen from the male plant. The trichomes are small, hair-like structures that cover the surface of the bud and produce the resin that contains the cannabinoids and terpenes.


The calyx is the outermost layer that protects the flower. Consider it as a layer of protection for the buds. It shields the inner parts of the flower as it develops and helps to prevent damage from pests and environmental factors. The calyx is also the site where trichomes grow. The size and shape of the calyx can vary depending on the strain of cannabis.


The pistil is a small, hair-like structure that grows out of the calyx. The primary function of the pistil is to collect pollen from male cannabis plants during pollination. However, for female cannabis plants, the pistil serves another purpose — to catch and hold the pollen that has been released by male plants.

The pistil also helps you identify the sex of the cannabis plant. Female plants will have long, white pistils that grow out of the calyx, while male plants will have smaller flowers that produce pollen. In addition to their reproductive function, pistils are also important for the visual appearance of the cannabis flower, as they can add color and texture to the overall appearance of the bud.

The shape and size of the pistil can vary depending on the strain of cannabis and can also change as the flower matures. When the pistil first emerges, it will be thin and white, but as the flower matures, it will start to turn a darker color, such as red or orange, or even amber.


The stigma is the sticky, bulbous tip of the pistil responsible for catching and holding pollen during pollination. 


Trichomes are small, hair-like structures that grow on the surface of the calyx and other parts of the cannabis flower. As you already know, they produce the resin we all love. The sticky resin contains terpenes and cannabinoids that produce medicinal and psychoactive effects. Terpenes are responsible for the bud’s taste and smell, while cannabinoids take care of the potency. 


The bract is a small, leaf-like structure that grows at the base of the calyx. Its primary function is to protect the developing flower from pests and environmental factors. Bracts are also covered in trichomes and can be a good indicator of the quality and potency of the flower.

5. Seeds

Cannabis seeds

The seeds of the cannabis plant are the reproductive structures that contain the genetic information necessary for the plant to reproduce. They are typically small and hard, with a brown or gray color. The seeds are covered in a tough, protective shell called the seed coat, which protects the embryo inside. 

The embryo is made up of a small plant that will eventually grow into a new cannabis plant. Although we growers use seeds primarily for cultivation, they are also a nutritious food source that contains high levels of protein, fiber, and healthy fats.

Cannabis plants are dioecious, meaning they have separate male and female plants, and sexual reproduction occurs when pollen from a male plant fertilizes a female plant. The male plants produce small flowers that release pollen, which is carried by the wind or insects to the female plants. The female plants have pistils that catch the pollen, and the fertilized pistils develop into seeds.

Once a female cannabis plant has been pollinated, the calyxes surrounding the seeds will begin to swell, and the seeds will begin to mature. The seeds are encased in a hard, protective outer shell, which can vary in color from light beige to dark brown, depending on the strain of cannabis.

The seeds themselves contain all the genetic information necessary to produce a new cannabis plant, including the characteristics of the parent plants, such as their growth patterns, flavor, aroma, and potency. When the seeds are mature, they will fall off the plant, or you can harvest, dry, and store them for later use.

Seeds can be used for a variety of purposes, including growing new cannabis plants or extracting oil and other compounds. However, seeds are generally considered less desirable than the flower of the cannabis plant when it comes to effects as they have low levels of cannabinoids and terpenes, meaning they can’t produce psychoactive or medicinal effects.

Summary: Cannabis Plant Anatomy: Get To Know Your Plant

As a grower, understanding the anatomy of a cannabis plant can help you produce high-quality yields. By knowing the different parts of the plant, their functions, and how they interact with each other, you can make informed decisions about how to care for your plants and optimize their growth.

For instance, understanding the structure and function of the roots can help you choose the right type of soil, nutrient mix, and watering schedule to ensure healthy root development. Knowledge of the stem and leaves can help you optimize light exposure and air circulation and also manipulate them for better results. 

If you’re a breeder or even a regular grower that wants to produce seeds to grow new plants, you must have a deep understanding of the buds and reproductive structures to pollinate the plant. You should be able to identify the best time to harvest to ensure the plant is potent and offers an experience that’s simply out of the world!

In addition, knowledge of the anatomy of a cannabis plant can help you identify and troubleshoot problems that may arise during the growing process, such as nutrient deficiencies, pests, and disease. By recognizing the symptoms and underlying causes of these issues, you can take corrective action before they become more serious and impact the health and yield of your plants.



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