In this study, morphological characteristics of two populations of Pike (Esox lucius) were compared in Anzali and Amirkelayeh wetlands at Southern Caspian Sea basin using morphometric and meristic characters. A total number of 57 speciemens of Esox lucius including 28 and 29 specimens from Anzali and Amirkelayeh wetlands, respectively, were caught by fyke nets. In this study 32 morphometric and 11 meristic characteristics were investigated and standardized first with Beacham formula, and then the data were subjected to a Principal Components Analysis (PCA), Discriminant Function Analysis (DFA) and UPGMA dendrogram. Based on PCA results, the two populations of Esox lucius were differentiated by 9 principal factors in morphometric characters. DFA revealed that the two populations were distinct in morphometric characters (87%). Also, the UPGMA dendrogram separated E. lucius populations of the Anzali and Amirkelayeh wetlands. It is possible that the different habitat conditions were the cause of distinct fish population of the two wetlands.