Spirlin,Alburnoideseichwaldii, is an abundant riverine fish in the southern Caspian Sea basin. The aim of this study was to investigate the morphological structure of Alburnoideseichwaldii populations in Karganrud and Chalus rivers based on morphometric characters, using truss network system. Sixty specimens of Spirlin from the rivers (30 specimens were caught in August 2010 from each river) were studied and compared. Fourteen landmarks were selected and 91 distances were measured between the landmarks on the left side of each specimen. Principal Components Analysis (PCA) and Discriminate Function Analysis (DFA) were applied to identify influential truss variables to differentiate between populations and sexes. The results showed that the morphometric characters were not useful for separating the sexes Discriminate Function Analysis separated these two populations. These variables seem to be under the influence of environmental factors such as water flow, the slope of the rivers, water physicochemical conditions and feed conditions of the fish populations