Black Mouth Croaker (Atrobucca nibe) is highly valued economically and There are very few published studies on genetic of this species. In the following study, the genetic diversity of Atrobucca nibe has been investigated using the PCR-sequencing method from two different regions of the Oman Sea, namely Chabahar in the Sistan and Baluchestan Province of Iran and Fujairah in the Fujairah Emirate of the United Arab of Emirates. 34 fish have been collected from the aforementioned regions. The DNA of the fish had been extracted through the Ammonium Acetate method and the quality of the DNAs were analyzed via the spectrophotometry and furthermore the quantity of the extracted DNA were assessed via electrophoresis. Polymerase Chain Reaction (PCR) was conducted on the targeted DNAs and later DNA sequencing was carried out. Subsequently, through sequencing it was discovered that the D-loop region in the mitochondrial DNA (mtDNA) of Black Mouth Croaker,contained 270 base pairs (bp). The nucleotide diversity discovered in the conduct of the following study was varied from 0.08 (Chabahar) to 0.1 (Fujairah), and the Haplotype diversity was estimated to be at 0.83 in Chabahar and 0.93 in Fujairah. Observed and expected heterozygosity averages were 0.47 and 0.69, respectively. So the observed heterozygosity had constantly been lower than that of the expected heterosygosity, reflecting the reduction in genetic diversity. Through observations of average levels of FST between the regions, it can be summed up that genetic differences do exist among the present populations. This study was showed there currently are two different populations of Atrobucca nibe residing in the waters of Sistan & Baluchestan and Fujairah.