The Philippines is among the most endemic-rich areas for all global biodiversity hotspots. Conserving that biodiversity presents multi-scaled challenges including the critical need for habitat and species level documentation as a basis for identifying conservation targets. This paper contributes to that need by describing the use of A Composite Bio-geographic Analysis (CBA) model to model the dynamics and inter-relationships between species distribution, nest, habitat and land use change, population distribution and access to the PA and to synthesize and evaluate data on the status and threats to the Philippine Eagle Pithecophaga jefferyi in the Mt. Hamiguitan Protected Area, one of the key biodiversity areas in the Eastern Mindanao Biodiversity Corridor (EMBC).