Killifish (Aphanius sophiae) of the Cheshme-Ali of Damghan and Shour River of Eshteherd were studied and compared from morphological point of view. For morphometric studies, 34 Truss morphometric measurements and  10 traditional  measurements  were made for each individual. Nine meristic traits were counted. Multi-variate analysis of variance (MANOVA) revealed a significant different between variables (P=O.OOO). Sexes and populations were using multi-variate analysis techniques such as Principle  Component Analysis and Discriminate Function Analysis based on morphometric variables. These variables seem to be under the influence of environmental factors such  as  temperature, salinity and feed condition. However, no separation was achieved based on meristic traits.