O. argyrogramma is the only species of the genus Oxynoemacheilus. It is distributed in the freshwaters of Iran and Iraq. The present paper reports a study carried out to investigate the genetic diversity and population structure of O. argyrogramma in Sepidbarg and Gamasiab river basins in Iran. 100 samples (50 samples from each river) were used in this survey. Microsatellite markers were increasingly used in population genetics studies. In this study, a total number of three microsatellite loci and two populations were studied. The average number of allele levels in the population was 13, which was more than the reported values for freshwater fishes. The expected and observed heterozygosity means were 0.652 and 0.876, respectively. Approximately all of the loci showed a deviation from the Hardy-Weinberg equilibrium. The genetic similarity and distance between the two populations were 0.346 and 0.707, respectively. According to the analysis, it seems that O. argyrogramma has a desirable genetic diversity in the investigated regions.