For several years, mud crabs of genusScyllahave been misidentified owing to their high morphological plasticity and the absence of distinct morphological diagnostic characters. The taxonomic confusion of genusScyllade Haan is considered to be a primary constraint to the development of aquaculture. Although genusScyllawas revised using morphological and genetic characteristics, taxonomy ofScyllaspecies occurring in India is still not clear. In this study, partial sequences of two mitochondrial genes, 16S rRNA and CO1 (Cytochrome C oxidase subunit I) in populations ofScyllaspp. obtained from eleven locations along the Indian coast were used to differentiate and resolve taxonomical ambiguity of the mud crab species in India. The sequences were compared with previously published sequences ofScyllaspp. Both trees generated based on 16S rRNA and CO1 indicated that allS. tranquebaricamorphotypes obtained during this study andS. tranquebaricasequences submitted previously from Indian waters reciprocally monophyletic with reference sequence ofS. serrata. Both sequence data and morphological characters revealed that the speciesS. serrata(Forskal) is the most abundant followed byS. olivacea. Further, the 16S rRNA and COI haplotypes of IndianS. tranquebarica obtained in the study significantly differed with the knownS. tranquebaricaby 6.7% and 10.6% respectively whereas it differed with knownS. serrataby 0.0–0.7% only, a difference that was not statistically significant. From these studies it is clear that “S. tranquebarica” commonly reported from India should beS. serrata(Forskal). [ABSTRACT FROM AUTHOR]