Coastal bluff, island grassland and coastal sage scrub are found on all three islets. In addition, West Anacapa has chaparral and woodland communities. Anacapa Island lacks the extensive crystalline iceplant community so prevalent on Santa Barbara Island. There are over two hundred different native and introduced species of plants on Anacapa Island. Some are rare and endangered. Seventeen of these plants are endemic to the Channel Islands, although none are specific to Anacapa Island. It is believed the Eucalyptus trees on Middle Anacapa were planted by a man named J.V. Elliott in 1885 and are now over a century old. These trees are native to Tasmania.

Anacapa Island has a wide variety of breeding land birds on the islands including the Red tailed Hawk and the American kestrel. The bald eagle and the peregrine falcon once lived on the island as well. There are eight species of birds on Anacapa Island that are endemic to the Channel Islands.

During the 1960's, the brown pelican suffered a critical population crash from the widespread use of DDT. However, with the ban of DDT and the restriction of visitors to West Anacapa breeding grounds, the pelican has made a remarkable recovery.