Balinsasayao Twin Lakes Natural Park (BTLNP) is one of the protected areas on the Island of Negros Oriental which is enormously rich in biodiversity due to different Lowland types formed along its elevation gradient. This study was conducted to better understand the composition and diversity of plant species in the natural park to improve conservation and management efforts of these remaining forests which are currently under threat from eco-tourism and other anthropomorphic influences. Within the 18 randomly distributed nested plots, a total of 351 species of plants were recorded. Of these, 183 species were trees, 54 herbs, 51 shrubs, 41 pteridophytes and 22 vines. The result of hierarchical cluster analysis showed differences in plant composition along the elevation gradient. There were 30 (9%) threatened species (vulnerable, endangered and critically endangered) and most of which were found in the submontane Lowland. Furthermore, the species diversity increases from lowland to sub-montane and eventually decreases towards montane Lowland. These results not only indicate the importance of BTLNP, but also highlights the submontane as a special area of concern due to the higher concentration of threatened and endemic species.