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The genetic diversity and population structure of Rutilus frisii kutum from three regions in the Iranian coastline and one region from Azerbaijan were investigated using microsatellite DNA markers. Genomic DNA from 140 specimens was extracted and using PCR approach nine loci with reasonable polymorphism were amplified. The results showed that the lowest mean number of alleles per locus (5.22) was observed in Tonekabon River and the highest (5.77) in Azerbaijan population. The observed heterozygosity in the Tonekabon River (0.625) population was higher than those of the other two populations in Iran and Azerbaijan population (0.473). Significant deviations from HWE were found at more loci in the Iranian populations than Azeri population. In spite of geographical distance, both the highest and lowest population differentiation (Fst) value was between Iranian populations not among the Iranian and Azerbaijan populations. The highest and significant was between Khoshkrud and Tonekabon (0.098) and the lowest and significant was between Khoshkrud and Gorganrud (0.062). The genetic distance was the lowest (0.27) between the Khoshkrud and Gorganrud populations, whereas the highest distance (0.493) was between Khoshkrud and Tonekabon River.The AMOVA analysis with consideration of 2 sampling regions (Iran and Azerbaijan) and 4 sampling locations (Iran: Khoshkrud, Tonekabon, Gorganrud and Azerbaijan: the Kura mouth) revealed that almost all of the variance in data namely 86% (p = 0.01) was within locations, genetic variances among locations was 12% (p = 0.01) and among regions was 2% (p = 0.01). The reported results could be of interest for management and conservation programmes of this species in the Caspian Sea.
