Population genetics has been recognized as a key component of policy development for fisheries and conservation management and aquaculture development. This study aims to evaluate the genetic diversity and population structure of native cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea, establishing the existing population distributions and contributing information to aid in the development of policy, prior to extensive aquaculture development. Microsatellite analysis of natural cobia populations in these two ocean basins shows similar levels of gene diversity at 0.844 and 0.837, respectively. All populations and almost all microsatellite loci studied show significant heterozygote deficiency. Genetic differentiation between local populations is low and mostly not significant (R ST = -0.0109 to 0.0066). The population shows no marked structure over the long geographic barrier of the Thai-Malay peninsula, either when analyzed using pairwise genetic differences or evaluated without predefined populations using STRUCTURE. Additionally, a Mantel test shows no evidence of isolation by distance between the population samples. The significant heterozygote deficiency at most of the loci studied could be explained by the possibility of null alleles. Alternatively, given the behavior of forming small spawning aggregations, seasonal migration, and hitchhiking on large marine animals, the population genetics could be complex. The population of cobia at each location in Thai waters may be inbred, as a result of breeding between relatives, which would reduce heterozygosity relative to Hardy-Weinberg frequencies, while some of these populations could be making long distance migrations followed by admixture between resident and transient groups. This migration would cause population homogeneity in allele frequencies on a larger geographic scale. The results suggest that 123Aquacult Int (2013( ) 21:197-217 DOI 10.1007 fisheries management for this species should be considered at both national and international levels, and until the possibility of local adaptation is fully investigated, policy development should apply the precautionary principle to ensure the preservation of genetic diversity and the sustainability of local and regional fisheries.