Green tiger shrimp (Penaeus semisulcatus ) is the most important shrimp of the Persian Gulf shrimp of the Penaeus genus. Based on studies on morphology and electrophoresis proteins are produced new subspecies of the tiger shrimp which called Penaeus semisulcatus persicus. In recent decades, the mitochondrial DNA is used widely as a genetic marker for determining the genetic structure of organisms and their evolutionary connect. The mian object of this molecular study is to investigate the evolutionary relationships between species and sub-species by sequencing 3850 bp (12200 to 16000). Genomic DNA was extracted from the ovarian tissue and swimming legs was used as a template. The polymerase chain reaction (PCR) with specific primers designed mtF8 / mtR8, mtF9 / mtR9 and mtF10 / mtR10 for amplification of approximately 1470, 1804 and 1573 bp was performed according to standard procedures. Amplified fragments were sequenced by the Sanger method. As a result of the restructuring of sequences by software EditSeq and SeqMan contact and overlap, species and sub-species nucleotide sequence was obtained. The nucleotide sequence of the species and subspecies have on the fragment of the gene ND1 and full length genes 16S rRNA, 12S rRNA and D-Loop region and tRNA molecules leucine (tRNALeu), valine (tRNA Val) and isoleucine (tRNA Ile) . Alignment and phylogenetic analysis of the sequence of species and subspecies, with 9 of Penaeidae (sequences extracted from GenBank) by using of the software ClustalW2 and MEGA 6 were analyzed and calculated. Genetic distance based on genes ND1, 16S rRNA, 12S rRNA, D-Loop region and the overall sequencing experiment, respectively0/168± 0.020 /, 0.080 ±00.008, 0.067 ± 0.005, 0.302 ± 0.023 and 0.139±0.006 was calculated. Genetic distance based on the above indicators in some species and sub-species was less Penaeus, and phylogenetic tree of all species and subspecies drawn to show the two branches. Results of this study revealed that the evoluti
