Sabah has experienced a rapid decline in the extent of forest cover. The precise impact of habitat loss on the conservation status of the plants of Sabah is uncertain. In this study we use the niche modelling algorithm MAXENT to construct preliminary, revised and final ecological niche models for Dipterocarpus lamellatus and Dipterocarpus ochraceus and combined these models with data on current land-use to derive conservation assessments for each species. Preliminary models were based on herbarium data alone. Ground surveys were conducted to evaluate the performance of these preliminary models, and a revised niche model was generated from the combined herbarium and ground survey data. The final model was obtained by constraining the predictions of the revised models by filters. The range overlap between the preliminary and revised models was 0.47 for D. lamellatus and 0.39 for D. ochraceus, suggesting poor agreement between them. There was substantial variation in estimates of habitat loss for D. ochraceus, among the preliminary, revised and constrained models, and this has the potential to lead to incorrect threat assessments. From these estimates of habitat loss, the historic distribution and estimates of population size we determine that both species should be classified as Critically Endangered under IUCN Red List guidelines. Our results suggest that ground-truthing of ecological niche models is essential, especially if the models are being used for conservation decision making.