Pholis fangi is an ecologically important fish species inhabiting Chinese coastal waters of Yellow Sea and Bohai Sea. To investigate the genetic diversity and population genetic structure of P. fangi, a fragment of 487 bp in the first hypervariable region (HVR-1) of the mitochondrial DNA (mtDNA) control region was sequenced for 181 individuals collected from Bohai Sea and Yellow Sea. A total of 18 polymorphic sites were detected, which defined 25 haplotypes. A moderate level of haplotype diversity ( h = 0.7052) and a low level of nucleotide diversity ( π = 0.0028) were detected. Both the phylogenetic tree and the haplotype network showed no significant genealogical structure difference among sampling locations. Pairwise F ST comparison and hierarchical molecular variance analysis (AMOVA) revealed that no significant genetic structure difference existed throughout the investigated regions, suggesting a high gene exchange among different populations. The results of neutrality test and mismatch distribution analysis indicated that a late Pleistocene population expansion (38000–127000 years ago) happened. Seasonal schooling migration may contribute to the genetically homogeneous population structure of the species.