﻿AbstractSea snakes of the genusHydrophisare important components of animal diversity in Iranian waters of the Persian Gulf and Gulf of Oman. Ten species ofHydrophishave been identified from the these waters and, in this study, genetic structure of seven species was compared with other populations in the eastern Indian Ocean and the West Pacific. We found that six species (H.platurus,H.cyanocinctus,H.spiralis,H.schistosus,H.gracilis, andH.lapemiodes) show high genetic similarity with conspecific populations in the Indian Ocean and Australia. However,H.curtusfrom southern Iran shows a high level of genetic differentiation from conspecific populations in Sri Lanka and Indonesia (0.6% and 6% genetic distance from Sri Lankan samples for16SandCOIgene fragments, respectively). Variation between Iranian and Southeast Asian populations may reflect new genetic lineages and suggest the need of further morphological evaluations to re-evaluate their taxonomic position.