Meretrix, a popular marine bivalve, features several species with significant ecological and commercial value, distributed in various marine habitats worldwide. Despite their importance, accurate global population estimates of these species are hindered by inadequate classification frameworks that often rely on external shell characteristics, which are susceptible to environmental influences. This limitation underscores the necessity for comprehensive research into the physiological and molecular attributes of these species for accurate identification. This study focused on identifying the local Meretrix species from Tarakan Island by analyzing their COI nucleotide sequences and comparing them with reference sequences in the BOLD and GenBank databases. The results demonstrate that the 14 specimens obtained with diverse morphological variations were found only within two major groups: Meretrix meretrix and Meretrix lusoria. These findings validate the efficacy of DNA barcoding as a tool for classifying marine bivalves, offering a robust framework for identifying unknown species, particularly in the Asian marine ecosystems. The study's approach and findings have broader implications for enhancing global marine biodiversity research and conservation strategies.