Pampus minor is an important commercial fish. Due to the similarity of external morphological characteristics among the genus Pampus species, P. minor has often been identified as the juvenile group of both P. cinereus and P. argenteus. While little genetic background on this species is known, this study was based on control region sequences and provided the first evaluation of the genetic signature of 264 individuals of P. minor from 11 populations along the coasts of China and Malaysia. The results indicate high genetic haplotype diversity and low nucleotide diversity in this species. Additionally, two differentiated haplotype lineages were identified in the P. minor populations. However, phylogenetic structures corresponding to the geographical locations were unable to be established. Analysis of molecular variance identified a vast majority of the genetic variation occurring within populations. F-statistic test value (FST) of pairwise indicated that great differences existed between the Chinese and Malaysian P. minor populations. For the Chinese populations, the genetic differences were insignificant with the exception of the Xiamen population, which is a marginal population. During the late Pleistocene, a population expansion of P. minor occurred. These expanded populations originated from the glacial refugium in the South China Sea and then rapidly occupied and adapted to their new habitat. The results of this study provide genetic information for ensuring the protection and management of P. minor resources.