DNA barcoding utilizing the cytochrome c oxidase subunit I (COI) gene was employed to identify the cave-dwelling bats in Tabaco cave, Sta. Teresita, Cagayan, Philippines, an unexplored site for molecular bat research. This study integrated preliminary morphological classification with confirmatory COI barcoding to identify species within this understudied assemblage. Three species from two families were identified: Hipposideros ater and Hipposideros lekaguli (Hipposideridae), and Miniopterus australis (Miniopteridae). Molecular validation corrected initial morphological assignments for several specimens, demonstrating high sequence similarity with reference sequences in the genetic databases, thereby resolving ambiguities within cryptic species complexes. The findings underscore the limitations of relying solely on morphology for species delineation in groups with overlapping phenotypic traits, such as Hipposideros and Miniopterus. This research provides the first molecular assessment of Tabaco cave’s bat community and highlights the critical role of integrative taxonomy, combining genetic data with morphological examination, for accurate biodiversity assessment. The results establish essential baseline data for the conservation of Philippine chiropteran diversity and advocate for an integrated framework to inform evidence-based conservation strategies for these ecologically pivotal and threatened taxa.
