Golden grey mullet, Liza aurata, is a non-endemic species with high commercial value in the Caspian Sea. This species showed sever mortality during recent years due to viral nervous necrosis. In the present study, six microsatellite loci (Mcs16Em, Mcs15Am, Muso10, Muso19, Muso22 and Muso27) were used to assess and compare the genetic structure of golden grey mullet in Gharesou and Gomishan regions (28 samples for each region) as well as dead samples from Gharesou region (28 samples). The polymorphism was observed in all loci. In the study of genetic diversity indices, the mean number of alleles and observed heterozygosity were obtained as 14.33 and 0.82, respectively. In addition, no significant difference of allelic diversity and heterozygosity was also observed between studied samples. 10 out of 18 tests showed significant deviation from Hardy-Weinberg equilibrium. The average amounts of inbreeding (Fis), genetic differentiation (Fst) and gene flow (Nm) indices were obtained as 0.07, 0.033 and 8.40, respectively. Furthermore, the lowest genetic distance and the highest genetic similarity were observed among the samples of Gomishan and Gharesou in that according to UPGMA dendrogram based on genetic distance, the samples from Gharesou and Gomishan were considered as a separate group from the dead samples.