Pampus minor is often mistakenly identified as the larva of Pampus argenteus or Pampus cinereus because of its small size. Despite its importance, studies on the population genetics of P. minor are not yet available. In the present study, the mitochondrial Cytb gene was employed to investigate the population genetics of P. minor collected along the coasts of China and Malaysia. The genetic diversity of all P. minor populations was moderate, and two major haplotype lineages were detected that were differentiated approximately 0.3 million years ago. These two haplotype lineages differed significantly in frequency distribution of Chinese and Malaysian populations, showing an imperfect geographical pedigree structure. Results of AMOVA also showed that the genetic differentiation was mainly among populations. According to the distribution of the haplotypes, an ancestral haplotype existed in both the Chinese population and the Malaysian population, further confirming that the Chinese and Malaysian P. minor populations originated from the same refuge in the South China Sea. A historical demographic analysis indicated that P. minor experienced a recent population expansion during the late Pleistocene period. Due to the need of P. minor to adapt to the diverse habitats, unique haplotypes were ultimately formed under the differing pressures of natural selection. This study is expected to provide a basis for future research of the population genetics of P. minor.