Abstract: In Iranian coastal waters of the Persian Gulf as a result of both direct and indirect human impacts such as uncontrolled or illegal hunting, sea turtle populations are drastically declining. Information on the genetic structure of marine species is essential for stock enhancement programs. To estimate the genetic diversity of the hawksbill turtle populations, the mitochondrial DNA control region was used as a matrilineal marker. The captured turtles (69 samples) were obtained from three different islands in the Persian Gulf. From all the samples DNA was isolated. The primers were selected based on a specific sequence in control region of mitochondrial genome. PCR products were restricted by various restriction enzymes and four different haplotypes observed. Measurement of inter-population genetic diversity and evolutionary distance between genotypes showed a low diversity in mitochondrial genome of hawksbill turtle in the studied regions. Therefore, the similarity between these three populations was significant. Present results provide evidences showing that significant genetic variation was not observed between these distinct populations and there is not even enough evidence to show the separation and diversion in the studied populations in haplotype level.