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.