Nuclear markers such as microsatellites have allowed the identification of conservation and management populations of the Hawksbill turtles. In present study, eight microsatellite loci were studied. 60 samples of hawksbill turtles. flipper from Shidvar and Hormuz Islands have been surgically removed and preserved in 20% DMSO buffer. DNA was extracted using DNP KIT and amplified by PCR methods. The average number of alleles in Shidvar and Hormoz were 7 and 7.37 respectively with range of 7-13. The average expected and observed heterozygosity was 0.77 and 0.46 respectively. The linkage disequilibrium and deviations from Hardy-Weinberg equilibrium have been tested. The Fst values was 0.048, showing a significant difference between the two sites (P<0.01). The genetic distance between populations was found to be 0.27, which indicates that the genetic difference among the studied populations is pronounced. These results together with highly significant RST of genotypic differences between these pairs of samples support the existence of different genetic populations of Eretmochelys imbricata within the Iranian Islands of the Persian Gulf.