Capoeta aydinensis can be diagnosed from its congeners in the Mediterranean Basin and in Central Anatolia by a combination of characters, none of them unique. It is closely related to and occurs geographically adjacent to C. bergamae, which is found from the Gediz River north to the rivers of the Biga Peninsula. It differs from C. bergamae by having 14-20 serrae along the posterior margin of the last simple dorsal-fin ray (vs. 21-26), a wider mouth (mouth width 32%-39% HL, mean 34% vs. 25%-33%, mean 30%), and a concave outer margin of the dorsal fin (vs. straight). It can be differentiated from C. caelestis from the Göksu River by having serrae along the posterior margin of the last unbranched dorsal-fin ray (vs. absent) and a shorter head (HL 22%-25% SL, mean 24% vs. 24%-27%, mean 25%). It further differs from C. caelestis and C. bergamae by the shape of the head and mouth. C. aydinensis has strongly convex dorsal profile of head (vs. slightly convex), slightly arched mouth (vs. moderately arched in C. bergamae), more arched mouth in female than in male C. caelestis, and straight or slightly convex lower jaw (vs. convex in C. bergamae; slightly convex in male, markedly convex in female of C. caelestis) (Ref. 115647).