<![CDATA[Accurate species identification is an essential foundation for effective fisheries management and conservation in Indonesia, particularly for near‑threatened species. This study aims to identify Bombay duck (Harpadon nehereus) from Cilacap Waters through morphological and molecular analyses, document its first record in Cilacap Waters, and provide a scientific basis for population studies, fisheries management, and conservation. Morphological identification was performed using physical characteristics such as shape, colour, and general features for morphometric and meristic analyses, guided by identification keys. Molecular confirmation was carried out through DNA barcoding of the mitochondrial COI gene. Primer Fish F1 and Fish R1 were used, along with the Sanger dideoxy sequencing method. The subfamily was confirmed by the presence of inner rays of the pelvic fin that are subequal or slightly longer than the outer rays. The genus was identified by the lateral‑line scales being enlarged and extending as a median lobe of the caudal fin. The primary rays of the caudal fin were without scales, and the body was compressed. The species was identified as H. nehereus because the pectoral fins reach beyond the origin of the dorsal fin. The obtained sequence (accession PV688437.1) showed approximately 96.928–99.495% identity with conspecific references in global databases and formed the same clade with other H. nehereus sequences in phylogenetic analysis, confirming its genetic identity. As the first confirmed record of H. nehereus in Cilacap, these findings provide essential baseline data for stock assessment, fisheries management, and conservation efforts in Indonesian waters.]]>
