In total,120 samples of adult common kilka were collected during the spring and summer seasons from two commercial catch stations in the South Caspian Sea .Fifteen sets of microsatellite primers developed from Clupeidae were tested on genomic DNA. Five primer sets (Cpa6, Cpa8, Cpa104, Cpa125, AcaC051) revealing polymorphic loci were used to analyze the genetic variation found in adults of the common kilka populations. Analyses revealed that the average number of alleles per locus was 13.1(range 5 to 22 alleles per locus in regions, Ne= 9.5). All sampled regions contained private alleles. The average observed and expected heterozygosities were 0.348 and 0.877, respectively. Deviations from Hardy-Weinberg equilibrium were seen in most cases. FST,RST, and gene flow estimates in AMOVA indicated significant genetic differentiation among seasons and regions (P≤0.01), indicating that the populations were divergent. The genetic distance between populations indicates that the genetic difference among the studied populations is pronounced. The data generated in this study provides useful information on the genetic variation and differentiation in populations of Caspian common kilka.
