Williamson County is home to five species that are listed as endangered.
Three of the endangered species are karst invertebrates that live in karst areas. A karst is the name for the honeycomb type limestone formations (including caves, sinkholes and fissures) that are typical in limestone geology.
The Bone Cave harvestman (Texella reyesi) is found primarily in Williamson County.
- The Tooth Cave Ground Beetle (Rhadine persephone) is a tiny, reddish-brown beetle that spends its entire life underground.
- The Coffin Cave mold beetle (Batrisodes texanus) is a small, long-legged beetle that lives in total darkness and has no eyes. This beetle is found only in Williamson County.
Karst Invertebrates Brochure
Two endangered birds also nest in Williamson County.
- The golden-cheeked warbler (Dendroica chrysoparia) is a migratory songbird that builds nests of juniper or cedar bark then binds them with collected spider webs. They winter in Central America but nests and breeds only in Texas.
- The black-capped vireo (Vireo atricapillus) is another migratory songbird that builds its nests just a few feet from the ground in brushy, transitional habitat.

The Georgetown Salamander (Eurycea naufragia) is a candidate species in the county that was petitioned to be listed as endangered. However, due to critical habitat acquisition under the Regional Habitat Conservation Plan the U.S. Fish and Wildlife recently lowered the listing priority for the Georgetown Salamander in recognition of the county's conservation efforts.