This pocket gopher ranges from southern California across the Baja California Peninsula, where four subspecies are recognized in a 2025 review. The male type specimen collected at Witch Creek, San Diego County, in 1893 was described with a dark brown back and tawny sides and chest.
Rhoads’s 1895 description calls the male from Witch Creek small, with a relatively short, well-haired tail and long, full fur. Its back was uniformly blackish brown, the sides and upper belly fulvous, the limbs, feet and lower belly line grayish, and the breast and abdominal midline strongly fulvous. Recorded measurements were 215 mm total length, 72 mm tail vertebrae and 28 mm hind foot.
In 1933, Grinnell described the San Diegan form then called Thomomys bottae nigricans as living in open ground across a wide range of soil textures. Its reported range extended from near sea level to 7,500 ft (about 2,290 m).
An extinction-risk assessment has not been added yet.