This thesis is a zooarchaeological analysis of Late Quaternary faunal assemblages from the Philippines, ca. 25,000 to 2,000 years ago. The research utilises several approaches within a broad ecological framework. The first element of the ecological approach is informed by zooarchaeology’s niche in palaeoecology and its application to modern biodiversity conservation. This approach is crucial for a tropical faunal region known for its exceptionally high levels of biodiversity and endemism but that also has a relative paucity of fossil studies. In this regard, the thesis aims to investigate the evolutionary and biogeographic history of these faunas. The second element of the framework uses the faunal subsistence record to explore human palaeoecology in the Philippines and its relevance to understanding indigenous ecological knowledge systems in the past. Using archaeofaunal material from Luzon and Palawan Islands, the study presents important fossil discoveries and palaeoecological insights into the dynamics of faunal change in the Philippines. The faunal analyses also allow the first attempt to construct Late Quaternary biostratigraphic sequences for the archipelago. For Palawan Island, the thesis presents an MIS-2 (25,000-20,000 cal BP) faunal record based on the re-excavation and re-dating of Pilanduk Cave. This record provides evidence for the presence of the tiger on Palawan during the Last Glacial Maximum and morphological confirmation of the presence of two locally extinct deer taxa. For Luzon Island, the study presents evidence from Minori and Musang Caves for previously unknown and extinct endemic giant cloud rats, as well as for the human translocation of macaques and palm civets. In line with the second element of the framework, the zooarchaeological analyses also provide foraging histories of local human populations in tropical island environments. The subsistence data present the responses and possible roles of humans in observed faunal and environmental changes. Human impacts are possibly implicated in the Late Holocene extirpation of the hog deer of Palawan and two endemic cloud rat species on Luzon. The subsistence records also present island-specific strategies for tropical rainforest foraging across the Holocene. Taken together, the findings offer diachronic perspectives on indigenous ecological knowledge systems as manifested in these changing local settings.