Common kilka Clupeonella cultriventris (Nordmann, 1840) is a brackish water and small pelagic fish species and is one of the most abundant fishes that live gregariously in the Caspian Sea. A total of 60 specimens of adult common kilka were sampled from two seasons. Fifteen pairs of microsatellites previously developed for A.sapidissima, C. pallasi, C.harengus, and S. pilchardus were tested for cross-species amplification on the common kilka. In this study, only five primer pairs were used successfully. Analyses revealed that the average of alleles per locus was 14.4. The average observed and expected heterozygosity was 0.153 and 0.888, respectively. All loci significantly deviated from H–W equilibrium. These results together with significant Rst. values for genotypic differences support the existence of different genetic populations along the Caspian Sea coast (Guilan Province).