Abstract: To assess the current status of germplasm resources in the crimson snapper (Lutjanus erythropterus), this study obtained D-loop region sequences from 90 individuals across five geographic populations (Shenzhen, Zhao’an, Zhanjiang, Beihai, and Lingshui), using PCR and sequencing. Results revealed that the D-loop region sequences ranged from 950 to 951 bp in length, with an AT base content of 63.2%. A total of 38 haplotypes were identified, demonstrating high haplotype diversity (H_d = 0.837–0.985) and low nucleotide diversity (π = 0.00725–0.01416). The genetic distances among the populations were small (0.00784–0.01324). Genetic differentiation analysis indicated that the fixation index (F_st) between most populations was less than 0.0500. At the same time, gene flow (N_m) exceeded the threshold of 1, suggesting no significant genetic differentiation among these populations. Neutrality tests revealed that the observed variation primarily originated within populations. A phylogenetic tree constructed using the Maximum Likelihood (ML) method showed no distinct branching or population-specific clustering, and the haplotype network exhibited no notable features, with haplotypes uniformly distributed across populations. These findings further support the absence of significant genetic differentiation among crimson snapper populations along the southeastern coast of China. Overall neutrality tests yielded significantly negative values, and mismatch distribution analysis displayed a multimodal pattern. Combined with goodness-of-fit analysis, these results suggest that the crimson snapper population has expanded, estimated to have occurred approximately 260 thousand years ago, during the Middle to Late Pleistocene. Given the importance of Lutjanus erythropterus to fishery resources and stock enhancement in the southeastern coastal region, it is recommended that future efforts prioritize monitoring its genetic background to prevent declines in genetic diversity from inbreeding and artificial release. Moreover, scientifically based zonal management measures should be implemented to ensure the sustainable utilization of its germplasm resources.