Native plants come in many shapes, sizes and types. From large trees to small herbs and flowering species, every part of the world has its own native plants that often grow nowhere else. Because native plants grow in the wild without the help of humans, they don't normally require much care in the form of water, fertilizing and pruning. You needn't prune annual native plants at all, especially if you want them to form seeds, which will drop to the ground and grow into next year's crop. But you can prune larger perennial natives to keep them tidy.
Prune large native plants such as shrubs and trees, in late summer and late winter to clean up and remove any dead, frost bitten or diseased branches and any that cross over another branch. You can prune up to 30 percent of most plants, according to Las Pilitas Nursery.
Prune smaller perennial natives, such as penstemons, in fall and after your final spring frost. In the fall, cut the plant back by about one-third, and in spring remove dead flower spikes down to the base of the plant.
Prune (deadhead) flower heads of all natives from which you want to collect seeds in fall. From California poppies to native pine trees, flowers and seeds normally form in spring through summer. Wait for the flowers to die and seeds to form, and then snip them off close to the base of the plant, or down to the branch from which they emerge.
Dispose of your cut plant parts in a compost pile or through your community's green waste recycling program. Or you can allow trimmed branches and seeds to remain in your garden---they can provide food to wildlife over the winter.
Research the needs of your specific plants. For example, it's a good practice to prune the California fuchsia in winter to within 1 inch of the soil, according to Yerba Buena Nursery. The coyote bush should be coppiced, or cut back to the ground, every 2 to 4 years.