In tropical regions, populations of many wildlife species have declined due to human activities. Thus, the paucity of studies addressing species recovery, species interactions such as herbivory and carnivory, and principal forces determining inter and intraspecific interactions, coexistence and adaptive evolution of vertebrates in the region is troubling. The fundamental issue here is how local interactions among organisms at different trophic levels—herbivores and plants, predators and prey—organize ecological systems and regulate their dynamics in tropical regions. To address this, we focus not just on the direct effects of the multitrophic interactions (e.g., herbivores and plants, predators and prey), but also on the feedback and indirect effects. We strive to understand how tropical vertebrates are influenced by spatial and temporal variation across seasons and anthropogenic perturbations. Using molecular techniques, notably DNA metabarcoding, we will expose the structure of interaction networks within the focal species. This research will enable a series of fundamental advances pertaining to the understanding of trophic ecology of the tropical vertebrates, inter and intra-specific competition and coexistence, and ultimately, the likely responses of the focal groups to human-induced perturbations and landscape changes. Armed with such knowledge, we seek to design and refine management strategies for conserving biodiversity and its associated habitats in tropical regions.