A Comprehensive Guide to Creating Your Own Hybrid Peppers

Let’s say you like serrano-level spiciness but appreciate pimiento peppers’ bulbous forms. Or, maybe you like ‘Shishito’ chiles’ skin thickness but like the habanero spice level. Combine pollen from one of these kinds with ovules from another, and you’re on your way to creating a new variety. 

Hybrid peppers are half one variety and half another. A pimiento and serrano cross may produce a new plant that grows large, red, spicy fruits, or it’ll create one that makes mild, sweet, thin-skin chiles. The unknown genetic factor makes this process exciting, as the only way to know what you’ll create is to try it yourself. You won’t know what peppers you create until your hybrid seeds grow into mature specimens and produce fruits.

Some tools ensure proper pollination, fertilization, and propagation. Growing your own hybrid peppers involves transferring pollen from one flower to another, so we’ll need materials that make this as easy as possible.

The herbal snips must have fine, thin blades so you can reach into pepper flowers without damaging their sensitive organs. When I can’t find my snips, I use cuticle clippers! You can similarly use anything that cuts and has small blades. With tweezers or your fingers, you’ll pick up these anthers and transfer them to a container.

The container helps you hold pollen as you transfer it from one flower to another. You’ll use your paintbrush to dust this pollen from male anthers onto the receptive female stigma of another flower. Anthers hold pollen, while stigmas lead to egg cells within the flower’s ovary. After pollination and fertilization, you’ll close the micromesh bags over the flowers. This prevents bugs and wind from spreading more pollen into the flowers you’re working with. 

If you don’t have any of these materials, fear not! You can repurpose your household items if they function similarly. Scissors work as snips, cheesecloth works for homemade micromesh bags, and you can use chopsticks instead of paintbrushes. Do it yourself and use what you’ve got!

Step 2: Hybridize During the Right Season

To gather hybrid seeds, we’ll need to wait for fully mature peppers to grow. This means you’ll want to hybridize new varieties as soon as flowers appear in spring or summer. If you wait until late autumn to transfer pollen, fertilized flowers may not grow mature seeds before your first fall frost. 

In other areas where peppers are perennial, you may hybridize varieties so long as flowers are present. Note, though, that species of Capsicum drop their flowers when temperatures soar above 90°F (32°C). Aim to hybridize during fall, winter, or early spring in warm winter zones.

In most gardens with winter chill, the best time to create new varieties is during spring. This gives your plants ample time to produce flowers, chiles, and seeds before extreme temperature swings start affecting pepper production. 

Step 3: Choose Your Varieties

What kind of pepper hybrid do you want to grow? Maybe you’d like a spicy bell pepper or a mild habanero. Whatever combination you’d like, this process starts when you select two varieties. 

Choose two kinds from the same species for the best results. Some species will cross-pollinate with others, albeit with varying success rates. One cross-species possibility is between cultivars of Capsicum annuum and C. chinense. ‘Pimenta Da Neyde’ is one example, as it’s a cross with purple chiles that taste like habaneros.

If this is your first time breeding peppers, I suggest using two cultivars of the same species. Look to your peppers’ scientific names to identify which species they’re in. Most common peppers like jalapeños, serranos, and bell peppers are Capsicum annuum. Others like habaneros and scotch bonnets are Capsicum chinense. 

Step 4: Isolate Pepper Flowers

Once you select your peppers you’re ready to start breeding! Peppers sprout bisexual or perfect flowers with male and female organs inside the same structure. This makes for easy hand pollination, but it also means we’ll have to cut some plant parts to avoid accidental fertilization. 

Inside bisexual flowers lie stigmas, which are receptive female organs that receive pollen. Surrounding the stigma are anthers that hold onto pollen. They dust it into the stigma, from where it travels down a tube. This tube is the style, and it connects to the ovary.  Inside the ovary, pollen combines with egg cells, or ovules, and successfully fertilizes them. After a few weeks, fertilized ovules swell into seeds to grow the next generation. 

When we breed peppers, we complete this process for flowers using the pollen and ovules of our choice. That way, we control the next generation’s genetics. Without our help, most of these flowers receive pollen from themselves and successfully self-fertilize. Self-fertilization creates genetically similar seeds rather than unique hybrid ones. 

Start making your hybrids by selecting recently opened flowers from both varieties you’d like to breed. You’ll want flowers open for a day or longer from the father plants and flowers open for less than a day from the mother plants. Flowers open for 24 to 48 hours already have pollen, so you’ll need fresh flowers for the mother and day-old ones for the father.

Step 5: Collect the Father’s Pollen

Select a flower full of pollen from a plant you’d like to be the father of your hybrid. The father donates half of the genetic material in your cross and has a major influence over your results. Select a father for disease resistance, fruit color, or chile flavor. 

With your father’s flower in hand, find its anthers. There are multiple anthers but only one stigma inside these bisexual flowers. They look like little pills attached to long filaments. Slice one to three of them off, and collect them and their pollen in your container.

If you’re making multiple crosses with many flowers, take as much pollen as you need without taking too much. Leave at least one or two anthers in the fathers’ flowers so they successfully fertilize themselves, giving you fresh peppers at season’s end. 

Step 6: Cut the Mother’s Anthers Off

Set your pollen jar aside while we look at the mother variety. It’ll produce chiles with our hybrid seeds that we’ll plant next year. This means we’ll need to monitor it until its peppers are ripe with fully formed seeds inside.

Start by selecting a recently opened flower on the mother variety. Check to see if there’s pollen inside—you’ll see yellow specks that dust off when you shake it. You’ll need one without pollen to ensure it only receives the father’s pollen we donate. 

Find the anthers inside the mother’s flower and slice them all off. You don’t need to collect these, so let them fall into the soil, where they’ll decay. Be careful when slicing so that you don’t hurt the stigma; it’s in the center of the flower and looks like a tube with a circular donut-like lip on its end. 

Step 7: Dust Stigmas With Pollen

Here’s the best part, where we transfer pollen like bees do! Gather your paintbrush and container with pollen, and bring them near the mother’s anther-less flowers. We’ll transfer pollen dust into the flower, simulating what happens when insects enter flowers. Instead of bugs, we’re the pollinators!

Using your paintbrush, delicately fill its bristles with pollen specks. You should be able to see their yellow color. Take your paintbrush and dust these specks onto the receptive stigma in the mother’s flower. Give it a good dusting more than once to ensure pollen travels down the tube-like style. 

One chile may have a dozen to hundreds of seeds; how many one produces depends on its variety. The more flowers you pollinate, the more hybrid seeds you’ll harvest. I suggest using at least two mother flowers; that way, you have one to fall back on if your first cross fails. 

Step 8: Bag the Flowers

With pollen in their styles, the mother’s flowers combine it with their ovules to start growing seeds. You’ll want to prevent other pollinators from contaminating your crosses and ruining your hard work. I use micromesh bags with fine holes for protection—you can use any sealing contraption that lets air in but keeps bugs out. Most mosquito netting or fruit protection nets work well.

Seal the mother’s flowers by placing bags over the entire flower, and take extra care not to break it. Close them around the stem. Then, watch and wait! You’ll keep bags on the flowers until they morph into small chiles. The fruits’ skins seal newly forming seeds and act as protective coverings.

You may leave bags on until harvest, but this sometimes leads to misshapen fruit. I recommend taking them off when you see green, young chiles. You won’t have to worry about accidental pollination, as the chile’s skin keeps pollen out while the ovules swell into seeds. 

After you take the bags off, hybrid peppers will look identical to the normal plants growing near them. Use a plant tag or stem label, and attach it above the top of your hybrid fruit. That way, when it ripens, you’ll be able to identify it from your normal crop. 

Step 9: Collect Seeds

After a month or two, your fertilized flowers will have morphed into ripening, colorful chiles. Inside them lie your hybrid pepper seeds! Harvest these chiles to gain access to your hybrid seeds. Snip fruits off their stems and bring them inside for processing.

Pepper seeds are easy to collect. They congregate where the stem connects to the inside of the chile. Harvest them by slicing open the peppers and collecting the seeds. Be careful with hot peppers, as their chemical capsaicin burns our skin. Use gloves while slicing them, and avoid touching your face or other sensitive parts. 

We’ll want to test our seeds’ viability before we store them. Put them inside a cup with water, and watch as they sink or float. Sinking seeds are viable while floating ones will struggle to sprout. Scoop floating ones out, then drain and keep the viable ones. Let them sit, and when completely dry place them in an airtight container. You can store these containers for up to five years in a pantry or closet that’s dark, cool, and protected.

Step 10: Sow Seeds

Peppers appreciate warm temperatures, so you’ll want to sow seeds as spring approaches. They’re perennial in zones nine and above—growers in these climates may start seeds year-round outdoors or in. For all other gardeners, plant them indoors two months before your last average frost date.

Sow pepper seeds a quarter inch deep in 5” pots. Water their soil well, then place pots under a bright windowsill. Try using grow lights if your windows don’t receive direct sunlight; peppers need six to eight hours of bright light to thrive. They also need heat. Use a seedling heat mat to promote the optimal soil temperatures for germination.

Your seedlings are ready for transplanting outside two to four weeks after your last frost date when temperatures are consistently above 55°F (13°C). Prepare a new home for them in raised beds, containers, or the ground. Dig a hole twice as wide and as deep as the rootball, then bury the peppers’ roots in the hole. Water well and keep their soil moist but not soggy thereafter.

Step 11: Repeat!

Congratulations! At this stage, you’ll be growing your first year’s hybrid peppers. Your seeds will sprout plants with traits from their mother and father. How these genes express themselves is highly variable, especially after the first cross. You may grow one plant with large, spicy chiles and another with squat, orange, and sweet ones. 

So, the first year you sow seeds, you won’t grow the ideal pepper you envision—or you might! The only way to know what you’ll get is to grow as many hybrid peppers as possible. Select your favorites annually, and cross-pollinate them further to get more desirable traits. You’ll repeat steps three through ten of this article every year until you’re satisfied with your hybrid’s traits.

Once peppers appear to your liking, let the flowers pollinate themselves. Save seeds from a few desirable plants and repeat the process annually until the genes stabilize. If a plant grows differently than you’d like, avoid saving its seeds and choose more favorable specimens. 

After eight years of growing new peppers, you’ll create a stable hybrid! This means you can save and grow its seeds, and they’ll produce plants identical to their parents. You’ll have a reliable variety like serranos, habaneros, or jalapeños. 

If eight years of intensive crossing seems intense, don’t worry! You can do steps one through ten one time, then save seeds annually from the peppers you prefer. Natural cross and self-pollination will stabilize the hybrids over time.