Tropical forests are now disappearing at an alarming rate that creates ecosystem unbalance such as climate change. In Sabah, currently there is only little emphasis on the conservation of individual plant species, which reflects a lack of information about their distribution and conservation status. Ecological niche models derived from Maxent will be used in this study to in conjunction with Sabah Land Use map 2008 to derive the percentage of habitat loss and construct a regional assessment. As a result, Shorea foxworthyi has the habitat loss at 54.6%, Shorea revoluta and Vatica maritima recorded 91.6% and 70.9% respectively. Since, ecological niche model (ENM) is a regional assessment, therefore Criteria A2, A3 and A4 is more appropriate in which the population reduction may not have ceased or may not be reversible. The most widespread lowland rainforest formation in Borneo is mixed dipterocarp forest (MDF). Ecological niche modelling approach have been recommended as a rapid assessment tool for constructing species; historic distribution during conservation assessment of dipterocarp species. Ecological niche modeling (ENM) can be a better conservation assessment method since it uses the regional assessment rather than global assessment. Besides that, it uses the high resolution of soil information as a variable which is an important element in this study.