Saving Pepper Seeds

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Peppers are remarkably beautiful fruits, and they display a remarkable variety of colors, shapes and sizes.
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Perfectly preserved Capsicum annuum seeds.
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Pepper varieties with exserted stigmas are more prone to out-crossing.
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Diminutive chiltepins (wild chile peppers).
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Habanero peppers can be air-dried.
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Chiles are strung together and hung to dry in ristras in the Desert Southwest.
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Wear gloves when slicing jalapenos.

From sweet bell peppers and mild poblanos to jalapeños and fiery habaneros, an amazing diversity of peppers can be grown in the vegetable garden — and saving pepper seeds is possible for many gardeners who wish to preserve variety in their gardens as well as save money.

Five domesticated species in the genus Capsicum are grown for their edible and ornamental fruits. Understanding their relationship to one another is crucial for the production of true-to-type seeds. Of the five species, three of them — C. annuum, C. frutescens, and C. chinense — are generally interfertile and are collectively known as the Capsicum annuum complex. They are able to cross-pollinate and so require isolation from each other. The other two species are less popular among gardeners. Of these two, C. baccatum may cross-pollinate with plants of the C. annuum complex, but C. pubescens will reproduce only with members of its own species. Because it’s relatively simple to isolate peppers by containment, gardeners often save seeds of many pepper varieties in one season.

Types of Peppers

Peppers are primarily grown for their edible fruits, which are consumed either while green and immature or after they’ve ripened. Additionally, dried peppers can be ground into spices, such as Hungarian paprika and chili powder. Peppers were originally classified into species based on morphology, and flower color was used at one time as part of the process of identifying Capsicum species, but these physical characteristics don’t correspond well to the sexual compatibility of the different types of peppers. Most domesticated peppers have purple flowers, solid white flowers, or white flowers with yellow spots.

Pepper types are often classified by the color, shape, size, and the thickness of the walls of their fruits, as well as their heat — that is, the intensity of their spicy flavor. Peppers’ heat comes from the compound capsaicin and is produced in the fruit’s placenta. Peppers are typically elongated but can range in size from diminutive chiltepins (wild chiles, pictured in slideshow) to 12-inch-long cayenne types. Fruits range in color from yellow, orange, and red to green and purple. There’s an almost endless range of market types of peppers, including sweet bells, anchos, frying peppers, tabasco peppers, serranos, and Thai chiles.

A Peppery Past

Part of the confusion about the relationship between the three species in the Capsicum annuum complex and the other two cultivated species, C. baccatum and C. pubescens, may stem from the fact that there were multiple domestication events for many of these species, and many wild Capsicum relatives were grown alongside these domesticated crops 8,000 years ago. Members of the C. annuum complex were most likely domesticated originally in regions of South and Central America. C. baccatum was domesticated at least twice, in western and eastern South America. C. pubescens was most likely domesticated only once, near modern-day Bolivia. From their centers of origin, peppers moved northward to the Caribbean and North America. In the 16th century, Spanish boats brought pepper seeds west to the Philippines, while Portuguese boats brought seed east to Africa, India, and Southeast Asia. Most of the chile peppers introduced to Europe didn’t come directly from the Americas but from India, Asia, and Africa via Turkish trading routes.

Growing Peppers for Seed

While perennial in tropical regions, peppers are generally treated as an annual crop in temperate and subtropical climates. Peppers germinate and grow best when soil temperature is above 75 degrees Fahrenheit. In most regions of the country, peppers are started indoors to provide the warmth they need and are transplanted out as weather becomes more suitable for growth. Plants are spaced the same in the garden whether being grown for eating or for seed saving. Viable seeds can be collected only from fruits that reach physiological maturity; many pepper varieties won’t have time to ripen in cooler or short-season climates.

Peppers have perfect flowers. Many of the newer cultivars of thick­-walled C. annuum sweet peppers tend toward self-pollination, while some types of C. pubescens peppers are self-incompatible. Between these two extremes, peppers exhibit a range of mating systems depending both on the variety and on the environmental conditions in which they’re grown. Like the flowers of tomatoes and eggplants, pepper flowers display various stigma positions — some are inserted, and others are exserted beyond the anthers (see photo in slideshow).

Prevent Cross-Pollination

Members of the Capsicum annuum complex (C. annuum, C. frutescens, and C. chinense) should be considered fully cross-compatible and should be isolated from one another. Although most C. baccatum cultivars will not cross with any of the above species, there are exceptions, and it’s best practice to also isolate cultivars of C. baccatum from those included in the C. annuum complex. In the garden, C. pubescens will not cross with the other domesticated species and does not need to be isolated from them. C. pubescens is easily differentiated from the other domesticated peppers by its black seeds.

Because peppers have a mixed mating system — with reported levels of out-crossing ranging from 2 to 90 percent — the recommended isolation distance for saving pepper seeds is in line with other species that reproduce through a combination of self- and cross-pollination. Although some modern sweet peppers can be properly maintained with a shorter isolation distance, the recommended isolation distance between pepper varieties — including those of cross-­compatible species — is 300 to 1,600 feet. Seed savers working toward the genetic preservation of a cultivar should consider using an isolation distance of half a mile.

Wild C. annuum populations are known to exist in extremely limited areas of southern Arizona and southern Texas. These plants can cross with domesticated Capsicum species (except C. pubescens) and require the same isolation distance as is recommended between domesticated cultivars.

If isolation by distance is not feasible, isolation by containment is a relatively easy method for controlling pollination. Individual flowers or flower clusters can be blossom-bagged before they open. Once the plants have set fruit and the fruits are visibly developing, the bags can be removed and fruits labeled so they can be identified when it’s time to harvest. Because many peppers produce small, solitary flowers — and these are located in the axils of rapidly growing branches — it may be difficult to affix blossom bags. Caging or covering entire plants may be an easier approach with these relatively short plants. One approach is to cover the plants while they’re still small and just as they’re about to begin flowering. When enough fruits have been set to fulfill the desired size of seed harvest, the covers can be removed. Fruits set at this point can be tagged for seed collection later, and any fruits that are set after covers are removed can be harvested for eating.

Because domesticated peppers are capable of self-pollination, viable seeds can usually be collected even if a gardener grows only one plant. The self-incompatible cultivars of the less frequently grown C. pubescens are the exception to this rule. The recommended population size to maintain a healthy variety of peppers is 5 to 20 plants. If saving seeds from a rare cultivar or working in genetic preservation, a population of 50 plants or more is recommended.

When roguing or selecting peppers, seed savers should consider important traits, such as plant habit, fruit shape and color, sweetness, and heat level of the fruit.

How to Save Pepper Seeds

Seed maturity in peppers is indicated by a color change in the fruit. Fruits are harvested as they ripen and can be processed immediately or held at 65 to 75 degrees in a protected location. Held at the ideal temperature, the seeds will continue to mature, but fruits should be monitored to make sure they don’t rot during this time.

Processing by hand allows gardeners to save pepper seeds from the fruits they eat. The simplest method to extract seeds from large peppers is to cut open the fruits and scrape the seeds off the core. The seeds can be rinsed to remove any pulp stuck to them, then immediately set out to dry in a thin layer on coffee filters in a warm, dry place with good air circulation.

Seed savers must be extremely cautious when cleaning hot peppers because capsaicin, the active component responsible for a pepper’s heat, is an irritant to mammals and burns eyes, skin, and lungs. Gloves, goggles, masks, and sometimes even a respirator should be worn for protection when extracting and cleaning pepper seeds.

Peppers are one of the few fleshy-fruited species that can be either wet-processed or dry-processed. Typically, seeds are extracted from thick-walled peppers using a wet process, while seeds from thin-walled peppers can be extracted using either a wet process or a dry process.

With smaller fruits, such as those of Thai chiles, whole peppers can be wet-processed in a blender or a food processor fitted with a dough blade. The peppers should be blended with ample water until the fruits have broken apart and the seeds have separated from the cores. The mixture can then be agitated and decanted several times until the water is fairly clear, and what remains is mostly seeds. The seeds should be rinsed and rubbed in a strainer under a strong stream of water until the seeds are free of any remaining pulp. The seeds should immediately be spread out to dry in a thin layer across a screen in a warm, dry location with good air circulation.

Thin-walled types of peppers, such as cayennes and habaneros, can also be dry-processed. After harvest, the fruits should be allowed to dry in a protected location until the flesh is brittle enough to break apart easily. In the Desert Southwest and other dry climates, chiles are strung together into what is known as a ristra and then hung to dry. Thick-walled peppers, such as bell peppers, cannot be dried in this manner because the moist flesh usually rots before the fruits are sufficiently dry enough to crush and remove the seeds. Once the fruits are dry, they should be crushed into a container and rubbed. On a larger scale, the seeds can be extracted by placing the dried fruits into a sack and treading on them until the fruits break open. The seed is then further cleaned by screening and winnowing. It’s important to wear gloves and protective gear throughout this process.

When stored in cool, dry conditions, pepper seeds can be expected to remain viable for two to four years.

Capsicum spp.

FAMILY: Solanaceae

LIFE CYCLE: Frost-sensitive perennial, typically grown as an annual in temperate climates

SUGGESTED SPACING: Same as when grown for eating

FLOWER TYPE: Perfect, self-­fertile flowers are borne singly or in small clusters

POLLINATION: Self-pollinated (autogamous) and insect-pollinated

MATING SYSTEM: Mixed mating system of self- and cross-pollination


FRUIT TYPE: Fleshy (berry)

SEED MATURITY: Occurs when fruits ripen to their final color; harvest individual fruits as they mature

METHODS FOR SAVING PEPPER SEEDS: Wet-process, or extract seeds from dried peppers

EXPECTED SEED LIFE: 2 to 4 years

ISOLATION DISTANCE: 300 to 1,600 feet


For viable seed: 1 plant

For cultivar maintenance: 5 to 20 plants

For genetic preservation: 50 plants

Reprinted with permission from The Seed Garden, edited by Lee Buttala and Shanyn Siegel, and published by Seed Savers Exchange, 2015. Learn how to save and share seeds from all types of plants — not just peppers — by visiting the Seed Savers Exchange website.

Mother Earth Gardener
Mother Earth Gardener
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