Lutjanus kasmira belongs to the family Lutjanidae. Over the past 20 years, the L. kasmira population in the South China Sea has been shrinking due to climate change, pressure from human activities, and inadequate food supplies. In this study, single nucleotide polymorphism (SNP) data obtained from restriction site-associated DNA sequencing (RAD-seq) were used to assess the genetic diversity of L. kasmira in Zhubi Dao (ZB) and Meiji Dao (MJ). The genome-wide nucleotide diversity (π) of the ZB

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... ulation and MJ population was 0.02478 and 0.02154, respectively. The inbreeding coefficient (Fis) of the ZB population and MJ population was −0.18729 and 0.03256, respectively. The genetic differentiation (Fst) between the ZB and MJ subpopulations was 0.00255102. The expected heterozygosity (He) of individuals from ZB and MJ was 0.33585 and 0.22098, respectively. The observed heterozygosity (Ho) of individuals from the ZB population and MJ population was 0.46834 and 0.23103, respectively. Although the ZB and MJ populations did not have significant genetic differences, the genetic differentiation between them was confirmed using population structure, phylogenetic, and principal component analyses. These results indicated that the genetic diversity of the ZB and MJ populations was relatively low at the genome level, and that their genetic differences were small.