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Aquilaria is a genus of about 20 species distributed mainly in the Indo-Malesian region. The genus Aquilaria belongs to the Thymelacaceae family of Indo-Malayan trees known for producing the world's most expensive oils, which are naturally occurring throughout the Philippines. Aquilaria is well known for the production of agarwood which is a highly wanted forest product of substantial economic value. In the Philippines, there is limited published information on the physical condition, habitat structure, and ecological threats of Aquilaria, which is a crucial factor to determine the optimum requirements to develop Aquilaria production system. Hence, this study was conceptualized to assess the habitat structure of Aquilaria as well as its conservation and ecological threats in the wild. Assessment, surveys and interview were conducted to gather on-site atmospheric data as well as ecological threats of Aquilaria in the wild. Soil collection was also gathered to analyzed soil properties. The results revealed that there were two species of Aquilaria documented in the study site, namely: A. malaccensis and A. cumingiana. Moreover, the soil chemical properties are not significant between different topographic expositions, but it is acidic and generally have low nutrient status. Furthermore, the conservation and ecological threats documented in the study site are unsustainable harvesting, a massive collection of regenerant, and inflecting damage of Aquilaria by punching nails or drilling holes in the trunk of standing mature tree. Therefore, it is highly recommended that Aquilaria should be protected, particularly A. malaccensis, since it is rare and considered a new record of occurrence to Leyte Island as one of the major findings of the study. The establishment of Aquilaria based production system is necessary as an option to reduce the rampant illegal poaching of agarwood in the wild but should be established on private land and registered with the Department of Environment and Natural Resources (DENR). [ABSTRACT FROM AUTHOR]