The Mount Makiling Forest Reserve (MMFR) is a biodiversity hotspot and listed as one of the 170 conservation priority areas established by the Philippine government. Its flora and fauna diversity has been reported, but knowledge gap has been identified concerning the bacterial communities associated with the flora and fauna. This study focused on ants (Hymenoptera: Formicidae), which are dominant in forest canopy and play essential roles in the ecosystem functionality. A metagenomic sequencing approach based on amplified V3–V4 regions of the 16S rRNA was employed to investigate the bacterial communities associated with five arboreal ant species collected from MMFR. The collected ants were identified as Dolichoderus thoracicus, Myrmicaria sp., Colobopsis leonardi, Polyrhachis mindanaensis, and Polyrhachis semiinermis. The sequence analyses revealed that Proteobacteria, Spirochaetes, Firmicutes, Bacteroides, and Actinobacteria were the most abundant phyla. Individual analysis of the bacterial genera associated with the five ant species showed that unclassified members of Rhizobiaceae, Orbaceae, and Burkholderiaceae were dominant in D. thoracicus. Unclassified members of Rhizobiaceae, Spirochaetaceae, and Ruminococcaceae were dominant in Myrmicaria sp. On the other hand, Candidatus Blochmannia, and Wolbachia were abundant in Camponotini ants C. leonardi, P. mindanaensis, and P. semiinermis. Bray-Curtis distance and UPGMA cluster analyses showed that the microbiomes of the Camponotini group clustered together, while D. thoracicus and Myrmicaria sp. exhibited unique bacterial profiles. Predictive gene profile analysis showed that the most functional categories were those associated with metabolism and biosynthesis of amino acids, pathways for metabolism of nucleotide, amino sugars and nitrogen, and utilization of different carbon sources.