In Palawan, the Philippines, a biological hotspot was turned into a protected area, called Cleopatra’s Needle Critical Habitat (CNCH). The most important goals of the CNCH are to conserve the rich endemic biodiversity and to maintain the culture of the Batak, a group of indigenous people who depend on forest resources for their livelihood. As resin extraction from Agathis philippinensis is a key component of the income of the Batak people, it is important to study the scope for sustainable exploitation of this species. This study focused on the effects of resin harvesting on the physical status and mortality of A. philippinensis trees in 15 subpopulations within the CNCH. These population characteristics were related to the intensity of resin harvest and the distance to communities. We found that the physical tree status deteriorated and the proportion of dead trees increased with harvest intensity and proximity to communities. These results indicate that overharvesting of the resource is taking place, which may lead to prolonged recruitment failure and population decline of A. philippinensis in the study area.