Genetic diversity and phylogeography of Hawksbill sea turtle was studied by using sequencing of the mitochondrial DNA (D-loop and tRNA pro region). 45 dead embryos were collected from the Qeshm (25 samples) and Kish Islands (20 samples) in the Persian Gulf. Analysis of sequence diversity showed over 890 bp of the mtDNA D-loop and tRNA pro region revealed 5 polymorphism sites and 7 haplotypes. Two new haplotypes were submitted on NCBI gene bank as Iran3 with GU997696 accession number and Iran7 with JN627023 accession number. Haplotype (h) and nucleotide (π) diversity was (h= 0.313 and π= 0.0006) for Qeshm Island and (h= 0.111 and π=0.0002) for Kish Island, respectively. Total haplotype diversity was calculated as 0.212, which had demonstrated low genetic diversity in this area. The Fst and P-value showed that Hawksbill turtles of Qeshm and Kish Islands are different populations. A comparison of our data with previous studies showed a relationship between the Persian Gulf and Indo-Pacific Hawksbill turtles and also sharp relationship with east Atlantic. Hawksbill turtles of the Persian Gulf have been migrated from the Pacific and the Oman Sea into this area. As a result, evidence of populations migration was not found from the West.