The Japanese threadfin bream, Nemipterus japonicus, the most abundant and crucially economic Nemipterus species is widespread throughout the Indo-West Pacific. The species has been studied widely for various aspects but genetic studies are scanty. This preliminary study contributes to the species phylogeography through the study of the genetic diversity and historical demography of N. japonicus populations from the Persian Gulf and Indo-West Pacific based on cytochrome c oxidase subunit I (COI) gene sequence. Grouping of the data into phylogenetic trees indicated that the Japanese threadfin bream consists of two reciprocally monophyletic phylogroups with 2.3% net sequence divergence which may qualify as cryptic species: clade I, consists of two sub-clades (Ia and Ib) occurs in the Persian Gulf and Western India, and clade II, which is restricted to the South China Sea. Historical and demographic hypotheses were raised to explain the observed phylogeographic pattern and population structure. Among the possible key mechanisms, sea level fluctuations driven by glacial episodes of the second half of the Pleistocene Epoch appear to have played an active role in initiating major phylogeographic separation. Apart from presumptive Pleistocene vicariance, a trend of increasing genetic differences with increasing geographic distance (i.e., isolation-by-distance) and regional differences in breeding season were also proposed as possible alternative scenarios. Since the baseline knowledge on the intraspecific genetic diversity and management and evolutionary significant units is the first step before any action to be taken, the basic findings provided by this research are particularly relevant to conservation efforts, fishery management and stock assessment