Mud crab () is an economically important aquaculture crustacean species in China and Southeast Asia countries. However, the catches of wild mud crabs declined sharply due to overfishing and environmental pollution. Therefore, it is necessary to understand the current genetic resources and population history of mud crab (), which would provide appropriate guidelines for genetic resource management and breeding programs. To achieve this goal, a total of 146 mud crabs from four geographic populations in the southeast coast of China were collected for whole genome resequencing to investigate the genetic diversity, population genetic structure, and runs of homozygosity (ROHs). Results showed that the nucleotide diversity (π) ranged from 0.00157 to 0.00160, with observed heterozygosity (0.248-0.257) approximately equal to expected heterozygosity (0.260-0.265), indicating that these populations were near Hardy-Weinberg equilibrium, albeit with relatively low polymorphism. The results of PCA, population structure, phylogenetic tree, and linkage disequilibrium (LD) analysis consistently indicated weak genetic differentiation among different geographic populations. ROHs detection revealed 47,142 ROHs in mud crabs, with over 60% shorter than 0.1 Mb. Moreover, the average genomic inbreeding coefficient estimated by ROHs (  = 0.0293) and homozygous sites (  = 0.0389) suggested relatively low inbreeding in mud crab populations. Notably, 29 candidate genes were identified in potential ROH islands, including growth and development-related genes ( and ), which may play an important role in the adaptive evolution of mud crabs. Overall, our results would provide valuable insights for conserving, managing, and improving the genetic resources of mud crabs ().