In order to study the genetic diversity of Thamnaconus modestus, a species of great commercial importance in Southeast Asia, the 5′-end hypervariable regions (423 bp) of the mitochondrial control region of T. modestus in nine geographical populations (248 individuals) were sequenced and analysed in this study. The target sequence fragment contained large numbers of polymorphic sites (87) involved in high levels of haplotype diversity (h = 0.97 ± 0.01) and nucleotide diversity (π = 0.0285 ± 0.0143). The genetic variations within populations (92.71%) were significantly larger than those among populations (7.29%). No significant genetic divergences were detected among the wild populations owing to their gregarious habits, strong moving ability, r-selection strategy. Significant genetic divergences were found between the cultured and wild populations, probably resulting from kin selection and aquacultural environment. Three significant phylogenetic lineages were identified, and the variation among lineages (56.90%) was greater than that among individuals within the lineages (43.10%), with the significant ΦST value (ΦST = 0.57, P = 0.0000). The results showed great and significant genetic differentiations among these three lineages, indicating that they may have independent phylogenetic dynamics. Dominant shared haplotypes that included individuals from each population and the median-joining network of haplotypes presented a star-like structure. Historic demographic analysis of each lineage showed that population expansion occurred after the Pleistocene glacial period. At the last glacial maximum, T. modestus in China seas was scattered across variable refuges, including Central South China Sea and Okinawa Trough.
