Genetic structure of golden mullet, Liza aurata, investigated in southern Caspian Sea using microsatellite markers. Totally 120 samples of adult golden mullet were collected from four regions, Anzali and Gomishan wetlands, Ramsar and Fereydunkenar coastlines. All primer sets as polymorphic loci were used to analyze the genetic variation. Analyses revealed that average of alleles per locus was 5.7 (range 3 to 9 alleles). Some sampled regions contained private alleles. The average estimates of inbreeding coefficient values of microsatellites were positive. The average observed and expected heterozygosity was 0.365 and 0.739 respectively. Deviations from Hardy-Weinberg equilibrium were in all cases. F-statistics and gene flow estimates in allele frequencies were 0.127 and 2.11 respectively. R_st and F_st estimates in AMOVA indicated significant genetic differentiation among regions. Genetic distance indicated that the genetic difference among the studied populations is pronounced. The data generated in this study provides the genetic variation and differentiation groups of golden mullet in south Caspian Sea.