Abstract
<title>Abstract</title> <p> The South China Sea is one of the world's most biodiverse shallow-water marine ecosystems, yet its true species richness remains underestimated owing to the continued discovery of new species, cryptic diversity, and unresolved taxonomic groups. Although molecular approaches have increasingly been applied to marine biodiversity studies, research in the South China Sea remains geographically biased toward its northern regions, with comparatively few investigations conducted in Malaysian waters. This study employed cytochrome c oxidase subunit I (COI) DNA barcoding to assess marine fish diversity within the Exclusive Economic Zone (EEZ) of the east coast of Peninsular Malaysia. A total of 508 specimens representing 225 species, 141 genera, 69 families, 25 orders, and two classes (Elasmobranchii and Actinopterygii) were analysed. Three species, <italic>Engyprosopon xystrias, Ostorhinchus septemstriatus</italic> , and <italic>Synodus nigrotaeniatus</italic> , are reported as new records for Malaysia and/or the South China Sea. Consensus species delimitation analyses identified 230 Molecular Operational Taxonomic Units (MOTUs), revealing cryptic diversity within <italic>Pomadasys maculatus, Turrum coeruleopinnatum, Nemipterus peronii, Maculabatis gerrardi</italic> , and <italic>Netuma thalassina</italic> . These findings demonstrate COI DNA barcoding complements traditional taxonomy, establishing a comprehensive COI-based reference library supporting biodiversity assessment, species identification, conservation planning, and sustainable management of marine fish resources in the region for research. </p>