Saving Pepper Seeds

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Although pepper flowers are chasmogamous, some varieties have inserted stigmas and are more prone to self-pollination.
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Of 29 sweet peppers evaluated at Seed Savers Exchange, 16 varieties had inserted stigmas and 13 varieties had exserted stigmas, such as this one (right). Exserted stigmas make a variety more prone to outcrossing.
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Pepper cultivars vary in both their immature and mature fruit color, but all peppers undergo a color change when their seeds ripen.
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The seeds of large-fruited peppers are easily extracted simply by cutting open the fruits and scraping the mature seeds away from the cores.
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Filled with advice for the home gardener and the seasoned horticulturist alike, “The Seed Garden: The Art and Practice of Seed Saving” provides straightforward instruction on collecting seed that is true-to-type.

The Seed Garden (Seed Savers Exchange, 2015) by Micaela Colley & Jared Zystro and edited by Lee Buttala & Shanyn Siegel brings together decades of research and hands-on experience to teach both novice gardeners and seasoned horticulturists how to save the seeds of their favorite vegetable varieties.

You can purchase this book from the MOTHER EARTH NEWS store: The Seed Garden.

From sweet bell peppers and mild poblanos to jalapeños and fiery habaneros, an amazing diversity of peppers can be grown in the vegetable garden. 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—Capsicum annuum, Capsicum frutescens, and Capsicum 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, Capsicum baccatum may cross-pollinate with plants of the Capsicum annuum complex, but Capsicum pubescens will reproduce only with members of its own species. Because it is relatively simple to isolate peppers by containment, gardeners often save seeds of many pepper varieties in one season.

Crop Types

Peppers are primarily grown for their edible fruits, which are consumed either while green and immature or after they have 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 do not correspond well to the sexual compatibility of the different pepper types. Most domesticated peppers have purple flowers, solid white flowers, or white flowers with yellow spots.

Pepper varieties 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 to 12-inch-long cayenne types. Fruits range in color from yellow, orange, and red to green and purple. There is an almost endless range of market types of pep­pers including sweet bells, anchos, frying peppers, tabasco peppers, serranos, and Thai chiles.


Part of the confusion about the relationship between the three species in the Capsicum annuum complex and the other two cultivated species, Capsicum baccatum and Capsicum 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 Capsicum annuum complex were most likely domesti­cated originally in regions of South and Central America. Capsicum baccatum was domesticated at least twice, in western and eastern South America. Capsicum 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 sixteenth 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 did not 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°F (24°C). 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 varieties will not have time to ripen in cooler or short-season climates.

Flowering, Pollination, and Seed Set

Peppers have perfect flowers. Many of the newer varieties of thick-walled Capsicum annuum sweet peppers tend toward self-pollination, while some types of Capsicum pubescens 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 are grown. Like the flowers of toma­toes and eggplants, pepper flowers display various stigma positions—some are inserted, and others are exserted beyond the anthers.

Variety Maintenance

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

Because peppers have a mixed mating system—with reported levels of outcrossing 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 (91 to 488 m). Seed savers working toward the genetic preservation of a variety should consider using an isolation distance of half a mile (0.8 km).

Wild Capsicum 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 Capsicum pubescens) and require the same isolation distance as is recommended between domesticated varieties.

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 is 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 are still small and just as they are 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 varieties of the less frequently grown Capsicum pubescens are the exception to this rule. The recommended population size to main­tain a healthy variety is 5 to 20 plants. If saving seeds from a rare variety 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.

Seed Maturity and Harvest

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°F (18 to 24°C) in a protected location. Held at the ideal temperature, the seeds will continue to mature, but fruits should be monitored to make sure they do not rot during this time.

Cleaning and Storage

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. 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 even a respirator should be worn for protection when extracting and cleaning pepper seeds.

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. Processing peppers by hand allows gardeners to save seeds from the fruits they eat.

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. Last, 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 be immediately spread out to dry in a thin layer across a screen in a warm, dry location with good air circulation.

Thin-walled 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 southwestern United States 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 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. A seed lot is then further cleaned by screening and winnowing. It is important to wear gloves and protective gear throughout this process.

When stored under 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 fruit (berry)

SEED MATURITY: Seed maturity occurs when fruits ripen to their final color. Harvest individual fruits as they mature.

PROCESSING METHOD: Wet-process, or extract seeds from dried peppers.


ISOLATION DISTANCE: 300–1,600 feet (91–488 m)

Population Size

For Viable Seeds: 1 plant

For Variety Maintenance: 5–20 plants

For Genetic Preservation: 50 plants

For more on seed saving, see our Seed Saving Guide.

Reprinted with permission from The Seed Garden, by Micaela Colley & Jared Zystro, edited by Lee Buttala & Shanyn Siegel and published by Seed Savers Exchange, 2015. Buy this book from our store: The Seed Garden.