Distinguished from all congeners, except Cottus carolinae, Cottus chattahoochee, Cottus confusus, Cottus hubbsi, and some populations of Cottus beldingii by the complete lateral line ending near the base of the caudal fin and dorsal fins not usually connected. Cottus specus only occupies geographically adjacent to C. carolinae and can be distinguished by a reduction in eye size: 1-5% SL in 98% of specimens (1-4% in 85% of specimens) versus eye size 5-9% of SL in 100% of specimens. Cottus specus possesses a significant increase in cephalic lateralis pore size, 92% above 500 mm (vs. 100% in C. carolinae between 200-500 mm) (Ref. 92978).