The species of Aquilaria cumingiana and Aquilaria malaccensis found in last remaining tropical rainforest of Leyte Island, Philippines, are facing threats in their natural habitat due to anthropogenic disturbances. To help address this problem, it is first necessary to understand the current situation and identify the limiting factors affecting their population. However, there is inadequate information available regarding the distribution and population dynamics of these species in the Philippines. We established four transect lines (2-km per transect), each containing nine sampling plots measuring 20-m by 20-m, positioned every 250 m, and monitored the size and survival of the two species within the sampling plots and along the transect lines during 2021-2024. A Generalized Linear Model (GLM) was used to assess the effects of light condition (relative photosynthetic photon flux density), elevation, the basal area of surrounding trees, and the distance from the community on the tree density of each Aquilaria species. Likewise, a Generalized Linear Mixed Model (GLMM) was used to examine the effects of the Aquilaria species initial size, light condition, elevation, and the distance on their growth performance. A total of 708 A. cumingiana and 71 A. malaccensis individuals were recorded, with average densities of 4.42 and 0.89 individuals 0.04ha^-1, respectively. Aquilaria cumingiana had higher population density than A. malaccensis, while the tree size of A. malaccensis was bigger and taller than A. cumingiana. The GLM analysis results showed that light condition had inverse effects on the density between species, showing significant positive effect on A. malaccensis and negative association on A. cumingiana. This suggests that A. malaccensis is sun demanding while A. cumingiana is shade tolerant. A higher population density of A. cumingiana was recorded at upper elevations among the four transects. Therefore, elevation might be a critical factor that influences population distribution pattern under natural conditions. Meanwhile, the GLMM analysis showed that distance had a significant positive effect on the diameter increment of A. cumingiana saplings and trees. In all transects, distance from the community is related to higher elevation that defines the natural habitat of A. cumingiana. Furthermore, the initial height negatively impacted the overall growth of A. cumingiana saplings and trees, and the significant negative relationship was found between distance from the community and density of A. malaccensis; indicating the disturbances due to poaching.