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Mussels play a significant role in the worldwide seafood industry. However, they are susceptible to fraudulent practices, especially substitution by other species due to relatively similar appearances among mussel species. Efficient and accurate identification techniques for mussel species have been developed for ensuring accurate labelling and preventing fraudulent activities. In this study, species-specific colorimetric based LAMP (loop-mediated isothermal amplification) assay targeting the mitochondrial COI gene of three mussel species including, Perna canaliculus , Mytilus galloprovincialis , and Perna virdis was developed and compared to conventional PCR assay. The LAMP condition was optimized by varying temperature and time followed by colorimetric observation and agarose gel electrophoresis. The specificity was tested against non-targeted bivalves and the sensitivity was evaluated by using DNA with concentrations ranging from 3.12 ng/μL to 0.003 ng/μL. In-house validation for cooked mussels was determined by using various conditions of different cooking methods, including boiling (B), steaming (S), frying (F), and canning (C). The developed LAMP assay provided accurate results at 63 °C for 30 min when visualized by colorimetric observation and agarose gel electrophoresis. LAMP and PCR showed similar specificity against three non-targeted bivalves while LAMP showed greater sensitivity than PCR for Asian green mussel and New Zealand mussels with the limit of detection 0.003 and 0.01 ng/reaction, respectively. Under optimal thermally processed conditions, both species-specific LAMP and PCR successfully authenticated three commercially important mussel species. The colorimetric LAMP assay developed in this study therefore is simple, rapid, and convenient for authenticating mussel products. • Colorimetric LAMP for accurate and efficient mussel species identification. • Identifies mussel species even after thermal processing. • More rapid than conventional PCR. • The detection limit for AGM is 0.003 ng, NZM is 0.01 ng, and MM is 3.12 ng. [ABSTRACT FROM AUTHOR]