This study used mitochondrial cytochrome c oxidase 1 in the identification of the fish prey from the gut samples collected from a stranding of a dead Irrawaddy dolphin in Pulupandan, Negros Occidental. Obtained consensus sequences were searched against the nucleotide database of NCBI and reference sequences, and sample sequences were used for generating the dendrogram and the pairwise genetic distances between species. Results showed that most of the sample sequences were 99% identical to the reference sequences.Eubleekeria splendens and Conger japonicus were the identified species in the stomach contents. E. splendens is a demersal and coastal species while C. japonicus is a demersal species and has not been previously recorded in the Philippines. Conflict in the taxonomy of the Conger genus may suggest that this may be identified as C. jordani. This study reports the first record of fish prey identification of the Irrawaddy dolphin in the country. Continuous monitoring of the Irrawaddy dolphin in the Guimaras Strait, including their feeding ecology, is needed to understand the population further and to improve their conservation.