Knowledge of the distribution and habitat preferences of a species is of paramount importance when assessing its conservation status. We used accurately recorded occurrence records and ecological niche modelling to predict the distribution of two threatened and poorly known small carnivore species that occur in Southeast Asia, the banded civet ( Hemigalus derbyanus ) and Hose ' s civet ( Diplogale hosei ), and analysed their spatial niche differentiation for habitat and elevation. We then identified possible anthropogenic threats, and used our modelling predictions to recommend surveying priorities. The predicted distribution of the banded civet was principally in lowland evergreen forest in southern Myanmar/Thailand, Peninsular Malaysia, Sumatra, Borneo and three Mentawai Islands (Siberut, Sipora and South Pagai), and for Hose ' s civet in evergreen forest across the higher elevation regions of Borneo. Our niche analyses suggested that there is a tendency for these two species to separate spatially along an elevation gradient: the banded civet is mainly found in lowland areas, whereas Hose ' s civet primarily occurs at higher elevations. Our study strongly indicated that these two viverrids are forest-dependent species that may be threatened by forest loss, degradation and fragmentation. Field surveys should be prioritised in areas where each species is predicted to occur and no records currently exist.