Restriction fragment length polymorphisms (RFLPs) of mitochondrial DNA were analyzed to determine intra- and interspecific genetic variability and genetic relationships among 3 species of mud crabs, Scylla olivacea, S. serrata and S. paramamosain. A total of 338 individuals, consisting of 107 S. paramamosain from 3 sampling sites in Japan and one site in Thailand, 119 S. serrata from 3 sites in Japan and one in Madagascar, and 112 S. olivacea from one site each in Japan, Indonesia and Thailand were analyzed. Analysis of mtDNA RFLPs using eight endonucleases revealed 24 haplotypes, and demonstrated distinct differences among the 3 species. Intraspecific haplotypec diversity and nucleotide diversity were low (0.187-0.313 and 0.0003-0.0007 for S. paramamosain, 0.176-0.418 and 0.0004-0.0015 for S. serrata, 0-0.278 and 0-0.0006 for S. olivacea, respectively), compared with the outgroups Portunus trituberculatus and Panulirus argus. We attributed this finding to short historical spread and small population size. Differences in diversity among there 3 mud crab species can be explained by the wideness of distribution range and population size. A high degree of inteaspecific diversity was found within populations, but not among populations distributed over a wide geographic range. Nucleotide diversity among the 3 species of mud crab was high (9.9-16.9%) . Dendrograms of relationships among haplotypes and populations clearly illustrated trends in divergence among populations and species. The dendrograms also showed that S. serrata and S. paramamosain were more closely genetically related to each other than either was to S. olivacea.