Mitochondrial DNA analyses of the golden snapper, Lutjanus johnii (Bloch, 1792), revealed two distinct population stocks in the South China Sea and the Strait of Malacca.

Population genetics plays a critical role in creating policies for managing fisheries, conservation, and development of aquaculture. The golden snapper, Lutjanus johnii (Bloch, 1792), is a highly commercial and aquaculture important snapper species. This study used mitochondrial markers D-loop (151 specimens) and Cytochrome b (Cyt-b, 120 specimens) from 10 populations, including populations from the east South China Sea, the west South China Sea and the Strait of Malacca to investigate the genetic diversity, population connectivity, and historical demography of L. johnii. High levels of haplotype diversity (D-loop: 0.974-1.000; Cyt-b: 0.711-0.952) were observed along with low nucleotide diversity (D-loop: 0.009-0.052; Cyt-b: 0.001-0.007), which suggests a population bottleneck was followed by an abrupt rise in population size. Genetic structuring was identified between populations in the South China Sea and its adjacent waters, compared to those in the Kuala Kedah population. Genetic structuring was consistently inferred from Bayesian inference trees, median joining networks (MJN), population pairwise Ф comparisons, F indices of genetic differentiation and a hierarchical AMOVA (Analysis of Molecular Variance). Demographic neutrality statistics and DNA mismatch distributions revealed species went through a sudden demographic expansion. Throughout the Pleistocene. Result from this study suggest that fisheries management for this species should take into consideration the genetic and demographic independence of the Kuala Kedah population. Policymaking should adhere to the precautionary principle to safeguard potential adaptive genetic diversity and ensure the sustainability of regional and local fisheries.