Mangroves are unique ecosystem exist in tropical and subtropical intertidal zones. They are most productive, diverse, biologically important ecosystem. Identification of mangrove species is of critical importance in conserving and utilizing biodiversity, which apparently hindered by a lack of taxonomic expertise. In the present study, we performed assessment of four mangrove species of Kerala, west coast India based on core DNA barcode markers, rbcL and matK. Present study does not support the species resolution among mangroves using plastid genes such as rbcL and matK. Our future work will be focused on evaluation of other barcode markers to characterize complete resolution of mangrove species and its identification.