Prior studies of species assemblages of fruit bats in the Philippines have focused on primary and disturbed habitats as the point of comparison. No studies to date have been conducted on assemblages of fruit bats within primary lowland forest vegetation types. This study aimed to determine the fruit bat assemblage in dipterocarp, mangrove and lowland ultramafic forest and their association with these vegetation types. We hypothesize that difference in the diversity and abundance of fruit-producing plants in these habitat types would influence the abundance and diversity of bats. The study was conducted in the Northern Sierra Madre Natural Park, Philippines from April to October 2017. Eleven species of fruit bats were captured during the study, in order of decreasing abundance: Rousettus amplexicaudatus, Ptenochirus jagori, Cynopterus brachyotis, Macroglossus minimus, Haplonycteris fischeri, Eonycteris robusta, Desmalopex leucopterus, Eonycteris spelaea, Pteropus vampyrus, Acerodon jubatus and Pteropus hypomelanus. Species richness was highest in dipterocarp forest (11 species), and lowest in the mangrove area (seven species), but species diversity was highest in the lowland ultramafic forest. The study suggests that species diversity and abundance of fruit bats in the different lowland vegetation habitats can be linked to their diet and morphology. Frugivores were strongly associated with dipterocarp forest and lowland ultramafic forest where fruit-producing plant diversity is high. Haplonycteris fischeri, C. brachyotis and P. jagori were more abundant in the dipterocarp than in the ultramafic forest. The abundance of nectarivores varied between vegetation types. Macroglossus minimus was more abundant in the mangrove while E. robusta and R. amplexicaudatus were more abundant in the dipterocarp and ultramafic forest. The difference in plant species composition and abundance may explain the variation in frugivore and nectarivore abundance between vegetation types. No pattern could be discerned for the large flying foxes (A. jubatus, P. hypomelanus, and P. vampyrus) because of few captures in each habitat, except for D. leucopterus, which was frequently captured in lowland ultramafic forest. The low captures of flying foxes may be attributed to the difficulty of capturing high-flying bats. Further research on foraging behavior, fruit selection by bats and the role of forest structure in determining the abundance and distribution of fruit bats is needed.