Lake Mainit is one of the key biodiversity areas in the country, its watershed area is a habitat of endemic and native plant species but is now threatened due to anthropogenic activities such as mining, kaingin and expansion of agriculture. This study assessed the diversity and community structure of plants in the lowland and upland of the two selected areas (Cantugas and Jabonga) of Lake Mainit watershed through a transect and quadrat method. A total of 321 floral species were identified distributed into 85 families. The taxonomically well distributed families were Arecaceae, Moraceae and Fabaceae with 18, 17 and 14 species respectively and most species were trees and shrubs (187 species). The highest species diversity, richness and abundance was observed in the lowland of Jabonga while the highest dominance was observed in the upland of Catugas. The floral species of Lake Mainit watershed are threatened by anthropogenic activities especially expansion of agriculture and tree felling for infrastructure developments regardless of their environmental roles and inherent benefits. Therefore, sustainable conservation efforts should be geared towards ensuring their continuous existence in order to maintain environmental integrity.