The endangered mission blue butterfly inhabits Milagra Ridge in Pacifica, Sweeney Ridge in San Bruno, Twin Peaks, and portions of the Marin Headlands. One of the first invertebrates to be protected under the Endangered Species Act, this small butterfly is an important component of area grasslands. Its host plant is silver-leaf lupine, and it is only in its mature flight stage for three weeks. Several butterfly habitat restoration projects are currently underway in the park involving non-native plant removal and native plant restoration. Threats to this species include development, trampling by excessive foot traffic, illegal off-road vehicles, and non-native plant invasion.  

The endangered San Bruno elfin butterfly occurs at Milagra Ridge and Montara Mountain near Pacifica, San Bruno Mountain in San Francisco, and near Alpine Lake and Dillons Beach in Marin County. Its host plant is stonecrop. Young larvae are tended by several species of ants that protect them from predators. These ants also groom the larvae and feed on a honeydew substance produced by the larvae.  Threats to this species include non-native plant invasion, trampling by people, lack of proper fire management, and development.

The Bay checkerspot butterfly inhabits Edgewood Park in the San Francisco Watershed. It has a wing span of little more than 2 inches. The forewings have black bands along all the veins on the upper surface, contrasting sharply with bright red, yellow and white spots. Their habitat is on serpentine soild where their host plant, dwarf plantain, grows. Males typically emerge four to eight days before females. Males can mate many times, while most females mate only once. Threats to this species include development and non-native plant invasion.