High genetic variations within populations and minimal to none gene flow occurrence in the studied populations was expected in this mangrove associated skipping fish. In conclusion, integrative identification provide better results to phenotypically ambiguous specimen like the larval fish and application of mitochondrial and nuclear gene markers were able to characterize genetic structure and evolutionary kinship of B. boddarti. Findings from this study allows better planning in mangrove utilizations, fisheries management and conservation effort of this high in commercial value mudskipper, B. boddarti.