Paracobitis atrakensis is diagnosed from other congeners in the Middle East by a combination of the following non-unique characters: absence of scales on the body, but presence of isolated scales on the dorsal adipose crest in a few of the individuals examined (vs. body fully covered by scales in P. longicauda and P. rhadinaea; posterior flank behind dorsal-fin origin covered by scales in P. malapterura, P. basharensis, P. molavii, P. persa and P. zabgawraensis). Both P. smithi and P. vignai lack scales on the body. P. atrakensis differs from P. smithi by having normally developed eyes (vs. absence ), a truncate or slightly emarginate caudal fin (vs. forked) and a dark brown color patter (vs. no color pattern). It can be separated from P. vignai by having a truncate or slightly emarginate caudal fin (vs. forked) and a roundish posterior nare opening (vs. slit-like) (Ref. 98825).