Sillago nigrofasciata, a small to moderate size nearshore species, is newly found along the eastern and southern coasts of China. The present study is carried out in order to analyze the population genetics of the S. nigrofasciata. The control region sequence of mitochondrial DNA revealing 73 haplotypes were obtained from 162 individuals collected at 8 locations along the coast of China. The whole S. nigrofasciata population along the coast of China showed a low nucleotide diversity (0.012) and a high population diversity (haplotype diversity) (0.943), and all the 8 local populations showed low nucleotide diversities (0.014–0.001), suggesting the protective measures are effective. The haplotypes of the 8 local populations were widely distributed in haplotype network diagram and neighbor-joining phylogenetic tree, while no branch associating with sampling locations was detected. Recent gene flow analysis showed asymmetric gene exchanges among local populations. The pairwise F ST values and unweighted pair-group method with arithmetic mean (UPGMA) tree revealed a certain amount of genetic difference among local populations. Moreover, analysis of molecular variance (AMOVA) reflected genetic differences between hypothetical subdivision groups. Neutral test and mismatch distribution of pairwise nucleotide suggested S. nigrofasciata may have experienced recent population expansion events. The historical geographic events associating with ice age may be the main explanation to the heterogeneity among local populations with short geographic distances, and the homogeneity among local populations with long geographic distances.