The Correct cuttlefish Sepia pharaonis (Ehrenberg, 1831) is an abundant cephalopod in Persian Gulf and Oman Sea. Despite the commercial and conservation importance of this species, information on population structure and diversity at the molecular level in S. pharaonis is scarce. Seventeen microsatellite loci from other species were analyzed to study genetic variation in populations of S. pharaonis from Iranian waters of the northern Persian Gulf coasts (Bandarabass, Lengeh and Bushehr). Eleven of the seventeen primer pairs failed to amplify, whereas six primer pairs successfully amplified: four pairs were polymorphic and two pairs were monomorphic. All loci were significantly deviated from Hardy—Weinberg equilibrium (P < 0.01). In the three samples of Persian Gulf analyzed, the four polymorphic microsatellite loci exhibited a mean allele number (N_a) of 7.5, mean expected heterozygosity (H_e) of 0.802 and mean observed heterozygosity (H_o) of 0.541.Weak genetic differentiation was present among the populations with F_ST values ranging from 0.020 to 0.31. This investigation represents the first microsatellite study of population genetics of this species in Iran, and the reported results could be of interest for management and conservation programmers of this species.