The Siah Mahi, Capoeta capoeta gracilis, is a widely distributed taxon in the south Caspian Sea basin (north of Iran) that has not yet been surveyed at the intra-specific level. Besides its ecological significance, this species is important for inland water fishing, aquaculture, sport fishing and zoogeographical studies. Here, we describe patterns of morphological and molecular differentiation among six populations of C. c. gracilis located in the Aras, Sefidrud, Shirud, Tonekãbon, Harãz and Gorgãnrud river systems in Iran. Univariate analysis of variance revealed significant differences between means of the six samples for 56 out of 60 morphometric ratios. The first two ordination axes of the mean ratios of the six samples (59.11% of total variation) separated all of the samples from each other, although not necessarily with any clear geographic pattern. The overall assignment of individuals into their original groups was high (88.6%). The proportion of individuals correctly classified into their original groups was 92.5%, 78.9%, 96%, 89.7%, 93.3% and 83.3% for Aras, Gorgãnrud, Sefidrud, Shirud, Tonekãbon and Harãz, respectively. Molecular clustering also grouped individuals of each sample either in the same cluster or the same sub-cluster. There was a large-scale congruence between results of the morphological and molecular analyses.