The significant decrease in wild mud crab population highlights the need to manage the resources and domesticate crabs. This paper presents the initial results of the domestication of mud crab Scylla serrata aimed at producing good-quality captive broodstock. The analysis of the genetic structure of the base population was done as a prerequisite for domestication. Adult S. serrata from the northern to southern parts of the Philippines (Cagayan, Camarines, Samar, and Surigao) were obtained for genetic diversity analysis and domestication. Analysis of molecular variance showed that differences in the genetic variability between the four populations were not significant. Moreover, no significant deviation from Hardy–Weinberg Equilibrium was ob...