With the collapse of inshore fishery resources, small economic fishes have become the major fish resource in the coastal waters of China. As one of the most important fish resources, big head croaker (Collichthys lucidus) has a wide distribution and high production in Chinese estuaries and is included on the List of China State Key Protected Commercial Sources of Aquatic Animals and Plants. However, the population structure of C. lucidus is still unclear, and knowledge of this is essential for decision-makers to sustainably develop the fishery industry. In the present study, the population genetic structure of C. lucidus in the coastal waters of China was examined based on mitochondrial cytochrome b gene sequences. A total of 342 individuals were sampled from nine localities from September to November 2019, and 174 haplotypes were subsequently identified. The median-joining network and neighbor-joining tree of haplotypes show two significantly divergent clades, Clade N and Clade S, which correspond to the geographical North group and South group, respectively. Analyses of molecular variance (AMOVA) also revealed significant genetic differentiation between the North and South groups (P<0.01). The genetic diversity results indicated that the haplotype diversity of the South group was higher than that of the North group (0.9418 vs. 0.8758); however, the results of nucleotide diversity showed the opposite outcome (0.0036 vs. 0.0041). Analyses of pairwise F_ST and N_m revealed significant genetic differentiation between the North and South group populations (P<0.05), with little gene exchange (N_m=0.06). The results of mismatch distribution and neutrality tests show that population expansion occurred for big head croaker along the coast of China in the Pleistocene era, and the expansion times of the North and South groups were estimated to be 7990–19900 and 26310–65770 years ago, respectively. The divergence time of big head croaker between the North and South groups was estimated at 345000–862500 years ago based on genetic distances. Historical events, biological characteristics, and other extrinsic forces (i.e., coastal currents) may all be associated with the current phylogeographic pattern of big head croaker in the coastal areas of China. In conclusion, the population structure of big head croaker along the coastal waters of China consist of the North group and the South group, which should be exploited and managed individually in fisheries.