In this article, I will discuss a simple and effective method for crossing peppers correctly. If you have enough space and time, you can cross two types of peppers to create a whole new species of pepper.

Purposeful plant breeding goes back to the beginning of agriculture. At the beginning of the work, the selection method was used. Basically, people grew starchy grains each year and selected the best quality crops for the next harvest.

Today, plant breeding is responsible for almost all fresh produce you can buy in the supermarket. From huge, gigantic apples to super-sweet grape tomatoes, hybridization was definitely part of their creation.

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Peppers have made great progress thanks to hybridization techniques. Examples include a super hot 7-pot primo and a not hot habanada pepper. Like many others, they were created through careful cross-pollination techniques and a lot of patience.

Habanada pepperHabanada pepper (not habanero).

I hope that doesn’t scare you, because crossbreeding exists in nature. Humans have simply observed and learned how plants have evolved on the planet over millions of years.

So today I’m going to share a basic method for crossing peppers. Although it is relatively easy, it takes a lot of time, dedication and patience to succeed.

Let’s go!

Before we get into the details, let’s put the overall process into visual form. This short tutorial will show you how to get through the peppers from start to finish. Remember, these steps represent many months and years of hard work.

I will explain each of the steps and basic terms in more detail. Nevertheless, this printed map can be a valuable resource that can be consulted throughout the process.

Click here for a high-resolution, printable version of this pepper crossing guide.

Why cross pollinate peppers?

First of all, I want to talk about why growing peppers can be interesting. Each grower usually has a different goal, while others just want to experiment and expand their hobby of growing peppers.

For example, some growers are obsessed with growing the hottest pepper. Others want to make a pepper that combines the shape and color of two types of peppers. Or maybe you’re more interested in getting a delicious taste.

Variety of pepper species.

All these traits are encoded in the genetics of each pepper plant. Stable interspecific pepper varieties share the same genetics, resulting in a new type of plant.

Other characteristics determined by genetics include plant productivity, harvest time, disease resistance, leaf color or variegation, and more.

Whatever your goal, it’s pretty clear that crossing peppers is interesting. I can make my own kind of peppers! It’s exciting, isn’t it?

The only downside? It takes a lot of time.

Anatomical and colour terminology

Before you begin, you should have a good understanding of the basic anatomy of the pepper blossom. By crossing peppers, we essentially disrupt the natural process of plant propagation.

Fortunately, the only part of the plant we need to understand is the flower. This is where the magic of the seeds is born.

A single pepper flower contains both male and female reproductive organs, making self-pollination possible.

Pepperflower fully openPepperflower fully open.

For pepper production, the flower must be fertilized with compatible pollen. In pepper plants, each flower can produce pollen and take it for fertilization. Therefore, each flower can go through the process independently.

Under normal conditions, individual peppers do well with self-pollination and fruiting. A gust of wind, a bee buzzing, or a running ant does that.

As we strive for cross-pollination, we must avoid self-pollination. This requires a basic knowledge of the anatomy of flowers.

Petals are modified leaves that surround the reproductive organs of the flower. Together they form the flower crown. They are usually white, yellow, green or purple peppers.

The pistil is the female reproductive organ of the flower. This is the central tube of the flower, which is usually white. At the end of this tube is the stigma, a hole that receives a single pollen grain to fertilize the flower’s ovary. The flower can then start to bear fruit.

Pollen is the male reproductive organ of the flower that is responsible for pollen production. In the case of peppers, they are usually white, yellow, orange or purple. They are in the center of the flower and enclose the pistil. When the anthers mature, they begin to produce powdered pollen.

Maternal and paternal predisposition. In crosses, the parent plant (mother plant) is the plant selected to produce the fruit. The father (paternal) plant gives off pollen to fertilize the flower of the mother plant. In other words: The father plants a pollinating flower on the mother plant, from which a fruit is produced.

Emasculation. To cross peppers safely, we need to make sure that the mother plant does not pollinate itself. In this process, the male genitalia are carefully removed from the flower of the mother plant. Anatomy of a pepper flower (partially sterilized).

Now that we have understood these basic concepts, we can move on to the method of crossing two varieties of pepper.

Crossed sweet pepper selection

First, you need to choose two types of peppers that are resistant and compatible with each other. Peppers of different varieties can sometimes crossbreed each other, but in some cases this can be more difficult or even impossible.

Look at this basic diagram to understand which species are compatible for crossing.

Selecting a compatible pepper

For simplicity, I recommend crossing two pepper varieties within the same species. Much of the hobby breeding community focuses on C. chinchilla because of its high heat and unusual shapes and colors.

Determine which properties you want to achieve by combining the two types. You can keep the shape of one pepper and color the other. Or maybe you want the high temperature of one to complement the delicious taste of the other. Setting goals at the beginning makes the long term process much easier!

Once you’ve chosen two varieties, it’s time to start planting.

Plant two peppers

Because we are going to isolate the flowers, you can plant your two varieties outside, right next to each other. In nature, the pollination process is imprecise, but we will master the important parts of it.

If you want to speed up the process, try planting in small pots to encourage early fruit. The downside is that small pepper plants tend to drop more flowers because of the plant’s limited energy.

Check out our guide to planting peppers from seed here.

Father against mother plant

As your plants grow, you may wonder which plant should be the father and which should be the mother. In other words: Which plant will give pollen and which will bear fruit?

Fortunately, there is a simple solution. I recommend going back and forth. In other words, both plants must be pollinated by the pollen of the other. Thus, the two resulting fruits can be used for the next generation of cultivation.

Depending on the resulting plants, you can determine which genetic lineage you want to pursue.

How to cross the sweet peppers

As soon as your two plants start to flower, you should be ready to unman them and pollinate them. In this guide, I will refer to Appendix A and Appendix B to make a distinction.

Pay attention: Make sure both plants are ready before you start. Plant A must have a flower that has just opened, while plant B must have an open flower that is actively producing pollen.


Find the flower of plant A that has just opened. How do you know that? Try to research the variety you are growing to see how big the flowers are and when they usually bloom. You can also have different flowers bloom to learn the pattern of the plant.

After selecting the flower on plant A, use tweezers or tweezers to remove the petals and anthers from the flower. Be careful not to disturb the stamp in the middle, it is fragile and can easily be damaged!

Remove petals and anthers from peppercorns.

When the degassing is complete, nothing should remain of the flower except the stem, calyx and pistil. It is now your mother flower, and it is ready to be fertilized with the pollen from the B plant.

Cross measurement of sweet peppers

Use dark colored utensils (a plastic spoon or a small kitchen jar is sufficient) to collect pollen from plant B. You can also use a small brush or cotton swab.

Place the collection bowl or spoon under the open flower of plant B. Shake or slide the flower to release the pollen into the bowl. The first click releases most of the flower’s pollen, so don’t miss it!

Gently transfer the collected pollen to the emulsified flower on plant A. Gently rub the pollen over the flower stick (pistil tip) being careful not to damage it.

Remember, it only takes one grain of pollen to fertilize a flower, so don’t be too aggressive. You can also repeat the pollination process for a few days to ensure that the mother flower collects pollen.

Colored insulation

Once you have brushed the pollen from the stigmas of plant A, the flower should be isolated from the surrounding flowers. It is extremely important to avoid other sources of unwanted pollen.

If the flower is exposed during fertilization, you cannot be sure of the cross. I use empty tea bags to gently seal and attach the flower to the flower stem.

Check the flower daily for signs of fetal development. Once the flower clearly begins to turn into fruit, the tea bag can be removed.


As long as the flower is isolated and covered, it is easy to determine what has been crossed. However, once the flower begins to bear fruit, it can be mistaken for other flowers.

So use a small piece of string to mark and identify the flower later. I recommend giving it a label with a specific cross (e.g. Banana [P] x Jalapeño [M]).

Reverse cross Repeat

I highly recommend repeating the process in reverse when plant A provides pollen to fertilize the emulsified flower on plant B. Wait for a suitable day when both plants will have sufficient flowers.

When the flowers have matured, they can be harvested to preserve the seeds. These seeds represent the F1 generation (1st daughter) of your crossbred pepper plant!

What if the flowers fall?

Unfortunately, all your hard work of sterilization and pollination can quickly end in the flower’s fall. It can be frustrating, but there are things you can do to prepare.

If you can, cross some mother flowers that are about to open. This ensures that you do not have fallen flowers. You can also remove the extra flowers that are about to open to avoid competition from the flowers on the mother plant.

F1 Generation

The two resulting fruits should not be harvested until fully ripe. Store seeds properly and make sure they are all properly labeled to avoid confusion.

If the two species you crossed are truly resistant species (heirloom, primitive varieties, etc.), then your first generation (F1) plants should be highly resistant.


Keep the different crosses separate and plant the seeds to grow the first generation. The two plants should be almost identical because of their genetic background, but you should always plant both anyway.

As the plants develop, you will begin to see what your new pepper cross will look like. I recommend that you take detailed notes on what you see.

Take notes on these characters (and anything else that is important to you):

  • Time to germinate
  • Growth rate
  • Color of the leaves
  • The time between sowing and harvesting
  • Moisture resistance
  • Heat tolerance
  • Budding degree (number of colours)
  • Appearance of flowers (color, size, etc.)
  • The shape of the fruit
  • Fruit size
  • Colour of the fruit
  • Performance
  • Trial
  • Heat level

There are numerous other small features you can monitor as your first generation grows. Just keep in mind what is most important to you!


When F1 plants bloom, keep the flowers isolated from other pepper varieties and pollen.

F1 pepper plants should be self-pollinating.

If your F1 plants are accidentally crossed with another pepper variety, the resulting fruits and seeds will contain an unknown genetic mesh. The original cross is lost, the genetics are uncertain.

To keep your F1 plants isolated:

  • Do not plant other varieties of peppers within 300 feet, or….
  • Isolate whole plants with cheesecloth or similar material to prevent cross-pollination.
  • Isolate individual flowers before they open and before they begin to bear fruit.

Choosing the perfect fruit and preserving the seeds

When your F1 plants start producing peppers, consider which peppers you want to keep for the F2 generation (2nd branch). Choose the fruit that matches the original purpose of your peppercorn.

Select mature F1 peppers and save the seeds for planting F2.

F2 Generation

It gets very interesting in the second generation.

The second generation is when the plants show the greatest variation.

Each seed you save from an F1 crop contains a different genetic makeup. That’s why I recommend planting as many seeds as there is room for, each in a separate seed box.

Tip: If you are looking for a specific leaf color, some F2 plants can be eliminated at the beginning of the process. For example, if some seedlings have purple leaves and others have green leaves, you can stop growing green plants at that point.

Once your F2 plants start to flower, you will need to isolate the flowers again. Plants must be forced into self-pollination to begin stabilizing genetics.

Choosing the perfect fruit and preserving the seeds

Due to the extreme variation in phenotypes at the F2 stage, selection of peppers to be stored may be more difficult than at the F1 stage. That’s why it’s so important to set goals from the beginning.

If you have a clear goal, you will have no trouble deciding which plants to keep. Taste the flesh of the peppers and save the seeds from the hottest pod.

If it is a color, keep the capsule that has the desired color. If it’s one size, choose the biggest or the smallest sleeve. To determine yield, weigh the peppers from each plant to determine the most productive.

Once the seeds are saved, you now have F3 seeds and the cycle continues. For F3, the process is repeated by planting as many seeds as possible, isolating plants, selecting ideal phenotypes and saving seeds for the next generation of plants.

How long does it take for the pepper variety to become stable?

After 7 or 8 generations of self-pollinated plants, the new chilli variety can be considered the most stable. However, if unwanted pollen has been introduced in any of the above steps, the resulting seeds may contain unknown and unstable genetics.

If you take your time and only grow one generation per year, this process can take up to ten years. However, there are ways to speed up the process if you want.

The easiest way to stabilize the variety faster is to plant it indoors and use smaller pots. The smaller the container, the sooner the plants will begin to bear fruit.

With smaller pots, plants can only produce one fruit at a time. So it is very important that you try to pollinate as many flowers as possible. You can also remove excess flowers that are not pollinated to avoid competition.


I’ve been wanting to write this article for a long time. I’m glad that at this point I feel confident enough to share my method.

Correct crossing of peppers is important for several reasons. In a world where amateur breeders rub flowers and hope for the best, a lot of the stable genetics get confused. Once purchased seed varieties may not produce the expected pepper varieties and stored seed may be unstable.

New varieties of peppers get this name and are sold with unstable genetics. Beautiful varieties appear without proper documentation of origin. If we all work together to achieve this, the catalogue of peppers will grow to everyone’s delight.

I hope you enjoyed this cayenne pepper guide. If you have any questions, suggestions, or even examples of cross-referencing that you would like to share, please contact us at [email protected].

Thank you!

Calvin's sketch


One of the original s! When Calvin isn’t gardening or learning about peppers and botany, he might be traveling to new places or making music.

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