In this study, the genetic relationships of 804 tarek (Alburnus tarichi) samples from a total of 18 populations, including the potamodromus and resident individuals from Lake Van basin in eastern Turkey, were studied by using nine microsatellite loci. A total of 93 alleles was detected, and the average number of alleles per locus was 10.3 +/- 3.39. The mean estimated observed and expected heterozygosity were 0.340 +/- 0.016 and 0.362 +/- 0.015, respectively, which indicated a low level of polymorphism. After Bonferroni correction (P < 0.0027), the multi-locus test applied to each population revealed that 12 out of 18 populations were in Hardy-Weinberg equilibrium (HWE) (P = 0.0120-0.9981). Analysis of molecular variance (AMOVA) showed more than 76% genetic variability within individuals and 19% among populations, which was significantly higher than zero (F-ST = 0.19), and furthermore, a low level of genetic variation was observed among individuals within populations (4.84%: F-IS = 0.06). Bayesian clustering analysis indicated that the total genetic variation grouped into 3 clusters. Additionally, the significance test results revealed that 11 of the 18 populations are threatened with extinction due to recent bottleneck events.We conclude that the tarek populations from the Lake Van basin can be classified into distinct genetic groups, based on microsatellite information. In addition, our results provide essential information for the development of a management plan that conserves the tarek's genetic diversity and achieves a sustainable fishery.