Abstract: The Japanese crimson seabream (Evynnis cardinalis) is a warm-temperate demersal fish species. To systematically assess the genetic resource status of this species under the pressure of overfishing, clarify its population genetic structure, and support the conservation and sustainable scientific management of fishery resources, we systematically analyzed the genetic diversity and population genetic structure of this fish species in the offshore waters of southeastern China based on mitochondrial control region (D-loop) sequences. A total of 220 specimens were collected from coastal waters of southeastern China between April and May 2025. Sequence analysis identified 168 haplotypes with 94 polymorphic sites. All geographical populations exhibited extremely high genetic diversity, with haplotype diversity of 0.994 9±0.005 8−1.000 0±0.044 7 and nucleotide diversity of 0.070 8±0.037 5−0.086 9±0.049 8. The Neighbor-Joining phylogenetic tree showed no distinct branching structure, and the haplotype network indicated extensive mixing among geographical populations. The Analysis of Molecular Variance (AMOVA) revealed that virtually all genetic variation (100.71%) was attributed to differences within populations, while the variance among populations was minimal and negative (−0.71%), showing a high degree of genetic homogenization. Low genetic differentiation coefficient (F_st=−0.000 28 to−0.013 03) and high gene flow (N_m=11.09 to 53.24) further confirmed frequent gene exchange among populations and a lack of significant population structure. Neutrality tests and mismatch distribution analyses indicated a population expansion during the Pleistocene, approximately 15,520 to 51,760 years ago. In summary, the study shows that E. cardinalis in the offshore waters of China has rich genetic diversity, and its populations possess strong environmental adaptability and recovery potential. There is no significant genetic differentiation among populations, with frequent gene exchange, and genetic evidence supports treating it as a whole for fishery resource assessment and management.