<![CDATA[The family Scombridae comprises economically important pelagic fishes traded across. However, taxonomic knowledge of Scombridae in Cenderawasih Bay remains remarkably limited. This study applied DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene for species taxonomy resolution. A total of 57 specimens were successfully sequenced and identified through BLAST against the NCBI database. We detected 12 species from 9 genera, namely Auxis thazard, Katsuwonus pelamis, Euthynnus affinis, Thunnus albacares, Acanthocybium solandri, Scomberomorus commerson, Gymnosarda unicolor, Grammatorcynus bilineatus, Thunnus obesus, Rastrelliger kanagurta, Rastrelliger faughni, and Rastrelliger brachysoma. Genetic diversity varied among the five focal species analyzed; Thunnus albacares and Auxis thazard exhibited the lowest haplotype diversity, indicating potential population vulnerability. Intraspecific genetic distances were below 2%, while interspecific distances exceeded 2%, confirming the effectiveness of the COI gene for species discrimination. Phylogenetic reconstruction produced well-supported clades consistent with established taxonomic relationships. The observed species composition in Cenderawasih Bay was dominated by widespread Indo-Pacific taxa. Notably, among the five tuna species (Thunnus spp.) known to occur in Indonesian waters, only Thunnus albacares and Thunnus obesus was detected in Cenderawasih Bay, raising the question of what ecological and oceanographic factors limit the presence of other tuna species. The ecological characteristics of Cenderawasih Bay are suggested to contribute to shaping the local Scombridae diversity patterns. These findings provide a fundamental genetic reference for Scombridae fisheries management and highlight the need for further oceanographic and ecological studies to understand the mechanisms driving species composition in the unique marine environment of Cenderawasih Bay.]]>
