5 Ways to Ensure the Purity of Your Seed

Isolation techniques

Why is seed purity so important? If you don’t keep your seeds pure, you never know what you’ll get the next year.

You may end up with pasty, yellow tomatoes when you thought you were growing large, juicy red ones. Or you may end up with an unidentifiable squash that tastes like watery pumpkin when you intended to grow a spaghetti squash. (Actually happened to a friend of ours… true story.)

To ensure the purity of your seeds, the correct pollen (‘male’) needs to fertilize the correct eggs (‘female’). How you do it depends on the type of plant, your garden size, your location, and the amount of time you have.

There are 5 basic techniques:

  1. Bagging
  2. Taping/Tying
  3. Caging
  4. Distance Isolation
  5. Time Isolation

Here’s a run-down of each technique for keeping seed pure, and the pros and cons of each.


Bagging is what I use most often in my own garden, because I can bag many flowers, and it’s inexpensive.


  • Inexpensive
  • Easiest method, especially for first-time seed-savers.
  • Bags take up little storage space.
  • Can be done anywhere… from balcony gardens to small farms.


  • Can’t be used for corn, spinach, and other wind-pollinated plants.
  • More time consuming.
  • Practical only for small-scale seed saving.

How To Use the Bagging Method

  1. Identify the plant you wish to save seeds from.
  2. Make sure the plant is self-compatible. (Check individual plants via our Compendium of Plants for Seed Saving)
  3. If it’s not self-compatible, be sure to identify the other plants needed to properly pollinate the flowers. (Usually flowers from other plants of the exact same cultivar.)
  4. Bag the flowers BEFORE they open. If you cannot get the bag to tie tightly around the stem, get a cotton ball, pull it out a bit, wrap it around the stem, and secure the drawstring tightly around the cotton.
  5. When the flowers have fully opened, if they are not self-pollinating, use a q-tip to transfer pollen around the flower (or from one flower to another).
  6. Re-bag the flower(s) until the fruit or the seed pod is beginning to form. (If they are self-pollinating, such as tomatoes, peppers, or beans, you don’t have to remove the bag and hand-pollinate, though doing so may ensure the production of seed.)
  7. Mark the pure flowers with a colored piece of string, and label.
  8. When fruit is fully ripe, or the seed pod is fully grown and dried, harvest the seeds and process using either the wet or dry method.


You do not have to use draw-string bags to bag your flowers. You could use a piece of kitchen muslin with a twisty tie, or a (clean) handkerchief with a length of string.

Whatever you choose to use, make sure it won’t deteriorate in the rain (eg. don’t use your typical paper bag), and it must be breathable (eg. no plastic bags). Anything that isolates the flower from being accessed by pollinators will work for the bagging technique.

If you intend to re-use the bags, especially for the a plant that could cross with the previously bagged plant, it would be a good idea to wash them. I prefer to wash mine without detergent, though I’ve never seen anyone say you shouldn’t use detergent.

To wash them, I place my empty drawstring bags in a mesh laundry bag, and wash in the dishwasher or in the washing machine. The heat will destroy any lingering pollen grains that may be in/on the bag. Allow them to air dry if they’re too delicate to go through the dryer.

Taping (or Tying)

I don’t particularly like taping because pulling off the tape rips the petals, most times, and I end up bagging it anyway to keep undesired pollen from entering the pistil, until the fruit is forming. With tying, the yarn/string may end up cutting through the petals. But if you’re careful, this method may work well for you. (And for all I know, it may become one of your favorite methods.)

Taped squash flower, now fully formed and ready to be hand-pollinated.

You can use masking tape to hold a flower closed until you’re ready to pollinate it by hand. This is most commonly used with plants in the Cucurbit family (melons, squashes, etc.).

A tied squash blossom (male).


  • Least expensive tools to get started with (masking tape).


  • Can only be used with larger flowers
  • Can rip the petals… and then you end up bagging anyway.

How to Use the Taping Method

  1. Tape the flower shut before it opens.
  2. Remove the tape and hand-pollinate the flower with a q-tip or a soft brush.
  3. Replace the tape until the fruit is forming. The tape can then be removed.


There are three ways the caging method can be used (alternate day caging, caging with hand pollination, and caging with introduced pollinators) but there’s an infinite number of shapes the cages can take. (I’ve seen some pretty creative solutions!)

After bagging, alternate day caging is my favorite method. It’s really is quite simple so don’t be intimidated to try it.


  • Can be used to produce pure seeds on a larger scale.
  • Can be left in place for plants that are self-pollinating.
  • Cages can be used for some plants that can’t be bagged.
  • Once cages are set up, alternate day caging takes very little time. (Hand-pollinating with cages will still take quite a bit of time.)


  • To make or purchase the cages initially is a larger up-front cost.
  • Depending on your cage design, the cages can take up a lot of space to store them when not in use.
  • The cage has to sit firmly on the ground, with miniscule gaps all around the bottom edges, to prevent pollinators entering.
  • All plants grow differently (tall and narrow, squat and spreading…) so you may need many different-sized cages.
  • You must plant in groupings that will match the size of the cages when you’re planning to save seeds.
  • Can’t be used for wind-pollinated plants.
  • The cage will prevent some sunlight from reaching the plants, and may slow their growth and development for the time that the cage is over the plant. Sometimes this can be for quite a long period, until none of the flowers on the plant are receptive to pollen anymore.

Homemade Cage Ideas

Homemade cages can take an infinite number of shapes and forms. Which makes them rather fun, really.


There are a couple of things to keep in mind when choosing your cages or the materials to make your own cages.

  1. You don’t want to lose too much light. Make sure the holes in the material are small enough to prevent insects from getting inside, without blocking out too much light.
  2. Your support structure must be strong enough to hold up the cage material.
  3. If the flowers of your plant are touching the sides of the cage, insects may be able to access them just enough to cause cross-pollination. You may have to stake, or bend and tie, the flower heads away from the sides of the cage to prevent this happening if your cage isn’t tall enough or wide enough.
  4. If your cage is light, make sure you stake the cage down somehow so it doesn’t get blown over without you knowing it.

Here are some ideas to get you started:

(affiliate links)
We often just use something like mosquito netting draped over a wooden or pipe framework. Even a plain, ol’ tomato cage will work (for smaller plants…).

If you don’t want to make your own, you could use food-covers like the ones pictured above (though those are limited in size).

Don’t forget your stakes to hold the whole contraption in place and a camel hair brush for hand-pollinating!

How to Use the Caging Method

As noted above, there are three ways to use the caging method. For all three, the cage needs to be in place before any flowers on the plant open.

You can make your own cages out of scraps of wood and any screening material that is small enough to prevent pollinators in, but will still allow light through.

Or you can use PVC pipes for the frame, which takes up less storage space when not in use because the pipes can be pulled apart. It is not necessary to buy fancy cages.

1. Alternate Day Caging

Alternate day caging is most useful when you’re sure there are no plant in other nearby gardens or in the wild that can be cross-pollinated with your plants (see Distance Isolation below), and when you have 2 or more plants in your garden that you want to prevent from cross-pollinating.

Some plants will set more seed when insects are allowed to do the work than they do with hand-pollination. If this is desired, then alternate day caging can be used, allows the pollinators to visit the flowers of each plant, without the risk of cross-pollination.

  1. Place a cage over the plants before any flowers have opened.
  2. Remove one cage each day, replacing it at night time.
  3. Remove the second cage, replacing it at night time.
  4. Repeat for several days until the plants stop flowering.


This can be done with even 3 or 4 cages, removing one each day, in a rotation. But the more cages that are used, and the less often the pollinators have access to the flowers, the lower the seed production will be. However, you will still get seeds, and you will spend less time than you would if you were hand-pollinating.

2. Caging with Hand Pollination

Rather than allowing pollinators to do the work for you, in alternate days, you can also pollinate the plants by hand. This method takes more time, as hand pollinating always does.

Hand-pollinating squash flowers.

The advantage to caging with hand pollination is that you can produce a larger quantity of pure seed with this method a bit more easily than with bagging, and you don’t have to worry about cross-pollination with plants in nearby gardens or in the wild.

  1. Place the cage over the plants before any flowers are open.
  2. Remove the cage (or climb in the cage, if it’s large enough) and hand-pollinate the plants. This can be repeated every day for several days to ensure the greatest amount of seed set.
  3. Replace the cage until the plant is no longer flowering.
  4. If you remove the cage before the plant is finished flowering, you can simply remove any other flowers that form before they open so they don’t end up setting seed, which then could get mixed in with your pure seed.

3. Caging with Introduced Pollinators

This is really only a good option for large seed-saving operations. It involves the use of cages, and instead of removing the cages to let pollinators access the plants, the pollinators themselves are placed in the cage to pollinate the plants within the confines of the cage.

Honeybees are often used. But honeybees that are used to being out in the open will often spend the whole day buzzing around the edges of the cage rather than pollinating the plants. I won’t go into the honeybee psychology here, or the ways to get around it, but it is rather interesting if you care to google it. 🙂

Distance Isolation

Bees, both honeybees and various wild bees, will likely not cross-pollinate plants if there’s a large enough distance between one variety and another. The distance varies, depending on the species/variety.

If you happen to live in an isolated area, with no neighboring gardens, and you’re sure of the wild plants that grow in your area, this method would work well for you.

If you intend to use distance, you’ll only be able to grow one variety of any species in your garden at any one time, but then you won’t have to worry about pollinating anything by hand, and you can gather your seed at the end of the season.

Lettuce is the one exception I can think of, because it requires such a small isolation distance, and the flowers are open for such a short time, that almost anyone can use distance as an isolation method for various varieties of lettuce. (Caging lettuce plants for the single day that they open will ensure pure seed.)


  • Easiest method, if you can be assured that no plants that can cross-pollinate with your plants are growing within the recommended distance (and that includes wild plants).


  • If you don’t know about wild or cultivated plants that are growing nearby, you won’t get pure seed and you won’t even know it.

How to use Distance Isolation

For recommendations on distance for each plant/species, see our Compendium for Seed Savers, which lists *every* plant by name and species, with details on distance requirements for isolation.

Time Isolation

Isolation by time works well as you know what plants are in flower within the distance isolation requirements.

It simply involves ensuring your plants are flowering at a time when plants that could possibly cross-pollinate with them are not in flower.

Last year we wanted to grow sweet corn, but our garden was surrounded by fields of dent corn.

Rather than give up our sweet corn for the year, I simply waited until 6-8 weeks after all the fields had been planted before sowing our sweet corn. That way, our ears of sweet corn would be forming when the tassels from the field corn were no longer producing pollen.

This technique works well as long as your growing season is long enough to allow for the delayed planting, while still leaving enough time for your crop to mature.


  • Takes much less time than some other methods (such as bagging with hand-pollination).


  • Not likely to be useful in short-season growing areas.
  • May be difficult to ensure purity of seed – there may be unknown wild or cultivated varieties that can cross.

How to Use Time Isolation

  1. Know what crops and wild plants grow in your area, and when they begin to flower.
  2. Plant your crops 4-8 weeks later than plants in your area begin to grow.
  3. When your plants begin to flower, be sure that other plants that can cross with them are not in flower – otherwise, do not save the seeds.


Recommended for Further Reading

Seed to Seed by Suzanne Ashworth and The Complete Guide to Seed Saving by Robert E. Gough (affiliate)  These are both great references to have on hand if you’re serious about seed saving!


4 Responses to 5 Ways to Ensure the Purity of Your Seed

  1. Bruce December 6, 2015 at 1:33 pm #

    Where do you get those pollination bags? They are the ones I have been trying to find for a couple of year?

    • Anni December 7, 2015 at 10:14 pm #

      They’re just party supply drawstring bags and tea bags that I purchased from Amazon.

  2. Ilayda February 14, 2016 at 4:17 am #

    We spent last friday stanitrg a whole bunch of our seeds and every morning I go check to see if any of the little sprouts have come through yet. So far, thyme is in the lead!I love gardening and I’m lucky to have a spouse who gets excited about it, too, and is more knowledgeable than I.Speaking of worms, my next step is building a little worm composter to live under the kitchen sink. Easier than turning over the big pile in the backyard. Whatever you learn about worms be sure to post!xoxo

  3. Carol September 21, 2016 at 1:12 pm #

    Ilayda, find the book “Worms Eat My Garbage” By Mary Appelhof Great book with great info. I have a bin in my bedroom. The one time I overfed them, I had a bit of gnat issue, but that got sorted out quickly and I’m a stickler about not overfeeding and making sure the bedding stays moist. It takes about 6-8 months (over winter here) to get a bin full of compost, but it’s worth it. My outdoor bin has never been this productive.

    Added bonus: They make the best roommates 😉

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