This species can be easily diagnosed at the genetic level from all its congeners in Iran by having 17 fixed molecular apomorphies (14 transitions and three transversions) in cytochrome b gene. In addition, it differs from Aphanius sophiae by having 61 fixed molecular apomorphies (46 transitions and 15 transversions). Males are distinguished from all other Iranian species by having only 7-10 wide clearly defined white flank bars, which is the lowest number of white flank bars among the Iranian inland Aphanius species, and bright to yellowish anal fin without clear white margin. Both males and females differ from other Aphanius species in Iran by having a significantly longer caudal peduncle and a smaller dorsal fin depth (measurements relative to the standard length) . The otoliths are diagnostic because they display a distinctive combination of characters such as a straight ventral rim, an angular to rectangular posteroventral edge and a wide but short and truncated rostrum. In addition, dorsal part of this species is longer than in the other examined species (Ref. 94548).