This paper describes and compares two species of Aphanius consisting A. vladykovi from Chaghakhor wetland (Chaharmahal-va-Bakhteyari province) and A. sophiae from Qomy-Abad Of varamine (Tehran province). In total, 59 morphometric and meristic characters were measured for each specimen. Ordination based on first and second factors resulted from Principal component analysis (PCA) revealed that two species are significantly different.(Males and females were compared separately to obviate sexual variation (A. vladykovi. 30 males and 26 females) (A. sophiae 22 males and 20 females). In females the characters consisting of predorsal length, preanal length, body depth, total length, head length, head width, prepelvic length and head depth were associated with the first component which accounted for 27% of the total variance. In males the characters consisting of head length, pre dorsal length, total length, preanal lengtn, head depth, postorbital length, head depth, pre pelvic length, caudal peduncle depth, mouth width and anal fin length were associated with the first component which accounted for about 33 % of the total variance in scores.