Anguillid eels are high-value food fish with 16 known species worldwide. Due to its taxonomic ambiguity and insufficient data on species composition, this family of freshwater eels were inadvertently regarded as a single species. This study collected 63 freshwater eels at 3 life stages (glass eel, elver, yellow eel) from Cagayan River, Philippines, to evaluate the accuracy of morphological identification in comparison with molecular analysis. Morphological results displayed clear distinctiveness between Anguilla bicolor and Anguilla marmorata despite some overlapping physical characteristics between Anguilla marmorata and Anguilla luzonensis. Phylogenetic analysis revealed that 15 out of 23 glass eel specimens were molecularly identified as A. marmorata, while 8 were identified as A. bicolor pacifica. For elver specimens, there were A. bicolor pacifica (n = 10), A. marmorata (n = 8), and A. luzonensis (n = 2). For yellow eels, there were A. bicolor pacifica (n = 10) and A. marmorata (n = 10). The results showed the inaccuracy of morphological identification in determining the richness and composition of Anguillids, which otherwise proved that molecular analysis is a more reliable approach in identifying freshwater eel species.