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, but no information is available on genetic differences within the subspecies populations. This study was designed to evaluate variation and differentiation in the Tajan River and investigation Shahid Rajaii dam effects upon Siah Mahi. A total 65 specimens were collected by electeroshocker set that 31 individual related to up stream station and 35 individual related to down stream station. Ten random 10-mer primers were primarily scored in 5 individuals from each of two stations and finally 6 primers, which shown polymorphic pattern repeatable, were selected and use in the final analysis of two locations. Totally 89 polymorphic band (marker) gained. Lengths of PCR products were between 50-1000 bp. Analyzing the PCR product data shown that the mean difference between the two stations was 0.478. In view of the fact that in ./5 mean genetic distance between two species, separated those from each other, as a result related two stations in a large quantity separated from each other. Results of Principle Coordinate Analysis or PCOA showed that two stations are separated from each other. The unweighted pair group method with averages (UPGMA) dendrogram based on Jaccard´s index also showed these stations are separated. There are perfect similarities between results of morphometric factor and morphometric spacialities. Based on the results, we conclude that RAPD fingerprinting was a useful technique in genetic discriminating the population of Siah Mahi.