Siah Mahi, Capoeta capoeta gracilis, is a predominant fish in the river systems of the south Caspian Sea basin. Although there is evidence of the geographical divergence of this taxon, no information is available on morphological differences within the subspecies populations. The study was designed to evaluate this differentiation in the Shirud River system of the south Caspian Sea basin in Iran. A total of 120 fish specimens ( ‡ 180 mm) were collected from the Shirud River; 33 morphometric and 10 meristic characteristics were recorded for each specimen. The standardized data were subjected to a principal component analysis (PCA) and variables with eigenvector ‡ 0.74 used as input for analysis of clustering, which grouped the 120 fish specimens into five distinct clusters. The overall random assignment of individuals into their original groups was high (86.7%), indicating that these specimens are highly divergent from each other. The proportion of individuals correctly classified into their original groups was 90, 81.8, 85.7, 100 and 76% for groups 1, 2, 3, 4 and 5, respectively. There were significant differences in nine morphometic characteristics among the five multivariate groups. Pectoral-anal length was the only characteristic that, based on all possible pair combinations of the five groups, could be individually distinguishable. With regard to meristic characteristics, a Kruskal-Wallis test showed that there were no significant differences among medians of the five multivariate groups.