Belongs to the subgenus Oligocephalus and most closely related to Etheostoma asprigene. Can be distinguished from other members of the of the subgenus Oligocephalus by having the following characters: spinous dorsal fin base is longer in E. thompsoni than in E. asprigene, E. collettei and E. swaini, averaging >30% of standard length in males and females (<30% in in E. asprigene and other Oligocephalus compared) and the transpelvic width is distinctly narrower than in in E. asprigene, E. collettei and E. swaini; nuptial males of E. thompsoni have significantly shorter snouts and caudal peduncles, and narrower bodies than nuptial males of E. asprigene and other Oligocephalus compared. Nuptial males of E. thompsoni also differ from those of E. asprigene in fin and body coloration by having numerous small red blotches or flecks on the sides of body anterior to the dark blue bars that alternate with bright red bars on posterior part of body and caudal peduncle; the central blue-gray band of the spinous dorsal fin is nearly uniform in width (vs. narrow anteriad and progressively widens posteriad in E. asprigene); lateral areas of the belly and between blue bars on the caudal peduncle is a more intense red-orange than in E. asprigene; lastly, naked nape (vs. fully scaled nape in E. asprigene) (Ref. 93431).