Rajah Sikatuna Protected Landscape (RSPL), considered the last frontier within the Central Visayas region, is an ideal location for flora and fauna research due to its rich biodiversity. This recent study was conducted to determine the plant species composition and diversity and to select priority areas for conservation to update management strategy. A field survey was carried out in fifteen (15) 20 m x 100 m nested plots established randomly in the forest over limestone of RSPL from July to October 2019. Three hundred and sixty eight (368) species of plants were identified up to species level. This represented 327 angiosperms, one gymnosperm and 40 pteridophytes. Common plant families with more than 10 representative species were Moraceae , Meliaceae , Lauraceae , Dipterocarpaceae , Rubiaceae , Myrtaceae , Phyllanthaceae , Annonaceae , Araceae and Lauraceae . There were 93 (28%) endemic and 46 (14%) threatened species (vulnerable to critically endangered) observed. The cluster analysis and species accumulation curve suggests that plant species are not homogeneously distributed which implies that different management and conservation strategies should be implemented across RSPL. These results not only indicate the importance of RSPL, but also highlights areas with higher diversity and concentration of threatened and endemic species as a special area of concern. Furthermore, areas with high biodiversity value were recommended for immediate protection, while areas with low biodiversity value were recommended for reforestation programmes using species with high importance value.