Phylogenetic relationships among all described species (total of 5 taxa) of the shrimp genus Penaeus, were examined with nucleotide sequence data from portions of mitochondrial gene and cytochrome oxidase subunit I (COI). There are twelve commercial shrimp in the Iranian coastal waters. The reconstruction of the evolution phylogeny of these species is crucial in revealing stock identity that can be used for the management of fish industries in Iran. Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus species of marine shrimp. For this purpose, DNA was extracted using phenol-chloroform well as CTAB method. The evolutionary relationships among 5 species of the shrimp genus Penaeus were examined using 610 bp of mitochondrial (mt) DNA from the cytochrome oxidase subunit I gene. Finally the cladograms were compared and the resulting phylogenetic trees confirmed that the Iranian species originated from the Indo-West Pacific species. The Iranian species, which were not grouped with the other Penaeid taxa, seem to always form a sister-clade to the Indo-West Pacific species with strong bootstrap support of 100%. Although the Iranian species + Western Hemisphere clade is paraphyletic in our gene tree, the bootstrap support is high. However, we still lack any comprehensive and clear understanding of phylogenetic relationships in this group.