The study used morphological and genetic approach for the DNA barcoding analysis of the inter- and intra-species relationships among catadromous Philippine freshwater eels. Past DNA barcoding studies on Philippine anguillid eels came from Northern Luzon. This study aimed to determine the DNA barcodes of the freshwater eels of the Philippines using the cytochrome c oxidase 1 (CO1) gene of the mitochondrial DNA. Specimens were collected from six sites in the Philippines. Four Anguilla species – Anguilla bicolor pacifica Schmidt, 1928, A. celebesensis Kaup, 1856, A. interioris Whitney, 1938 and A. marmorata Quoy & Gaimard, 1824 and one Monopterus species– Monopterus javanensis Lacepéde, 1800 were collected and identified. Morphological features varied from the taxonomic guides for Anguilla celebesensis and A. interioris with their body color and fin length. Genetic divergence estimates using Kimura 2-parameter substitution model showed an intraspecific variation of 0–0.4% and interspecific variation of 4.1– 27.6%. The ML tree generated was similar to the previous studies and indicated the monophyly of the Indo–Pacific freshwater anguillid eel lineage. This study also reports the first genetic record of M. javanensis sampled from Batac, Ilocos Norte, Philippines.