Effective stock assessment and fisheries management require clearness in their taxonomy for any species. Crabs are well known for its morphological plasticity and complex life cycles for which they became much contentious in their identification. Although crab fauna of Andhra Pradesh studied using different morphological and molecular approaches, still there were ambiguities with some species in India. The present study was carried out to find out genetic divergence and to validate phylogenetic position crab fauna of Andhra Pradesh by analyzing six partial Cytochrome Oxidase I (COI) sequences of mitochondrial origin. These COI barcodes were utilized to analyze the nucleotide frequencies, and evolutionary genetic divergence by following Kimura 2-parameter model employed in MEGA 6.0. A pair wise genetic distance among the species was found increasing with higher taxonomic levels. Nearest Neighbour distance was calculated using NCBI-BlastN, clearly demarcates its nearby species. Neighbour-Joining tree generated was incongruous with morphological taxonomy based on morphology emphasizing that multiple specimen inclusion in barcoding studies. Findings of this study demonstrated the efficiency of DNA Barcoding as molecular identification tool. So, it could provide us leverage for a better understanding in management and monitoring of crab diversity.