Domestication of a wild-caught aquatic animal is an evolutionary process, which results in discrimination at the genomic level in response to strong artificial selection. Although, black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used high resolution skim-sequencing based genotyping approach for investigating the genetic structure of 50 broodstock individuals of P. monodon species, collected from the five sampling sites (n=10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii (MMO) and Thailand (MT).