Otolithes ruber is one of the most important fisheries stocks of Persian Gulf that belongs to sciaenidae family. Thus identifying populations of this species is very important in order to preserve the genetic stocks of it. The studied area in this research was coastal waters of Persian gulf and Oman Sea, including Abadan, Boushehr, Dayyer, Bandar Abbas and Jusk. 5 samples of each area were collected. Genomic DNA of each sample was extracted from caudal fin and PCR was carried out for them with one pair of 16s rRNA primer. PCR products were sequenced. The results of this study showed low genetic differentiation between different areas populations, as the most significant (P<0.05) difference was observed between Jusk and Abadan and the least significant (P<0.05) difference was observed between Boushehr and Abadan. Genetic variance in three defined groups (first group: Abadan and Boushehr; second group: Dayyer and Bandar Abbas and third group: Jusk) was 20.13 of total variance. Estimated variance in comparison between 5 areas was 2.70 of total variance. The most observed genetic variance was in the populations of each area. This shows there is a valuable genetic diversity in different areas that make it necessary preserving this genetic stocks. In this study, there was a low genetic differentiation according to 16s rRNA gene. In general, the low amount of genetic differentiation of this species is relevant to lack of any barrier in Sea that cause geographical separation.