In order to assess the phylogenetic relationships of three rare species belonging to tribe Parablenniini was carried out, along the Coast of Oman Sea. Based on the type of habitats the specimens of Blenniid were collected from three sampling sites in the intertidal zones by Scoop and hand net in low tide and in sub-tidal zones by scuba diving and hand from 3, 6, 9, and 12m depths in September to March 2013. Totally 30 fish samples collected and deposited to the lab for further investigation.  Based on the available identification keys and morphometric characters three species of Parablennius cornutus, Parabelennius pilicorn, Scartella emarginata were identified. DNA was extracted from the basal tissue of the first dorsal fin, subsequently by using a specific fish primer 700 bp of Cytochrome Oxidase C subunit 1 (CO1)was amplified in polymerase chain reaction (PCR) and sequenced. After comparison of Iranian Blenniid species CO1 sequence with sequence of 25 species from GenBank, was concluded that Iranian species are paraphyletically in the clade Parablenniini and sub-clads of Scartella and Parablennius. Since the relationship of Parablennius with other blenniids is the subject of many studies to resolve the conflicts and ambiguities among them we selected these genera to investigate the sister group relationship among them as well as other genera and clads. This is the first time that morphologic and molecular study of the two genera Parablennius and Scartella have been carried out in Iran.