We used ecological niche modelling to predict the geographic distribution of the Indian Fox, a canid endemic to the Indian subcontinent. This little known canid, while not yet endangered, is threatened due to rapid habitat loss and poaching throughout its range. We analysed 58 known occurrence locations from survey data collected from three states in peninsular India using the software Desktop GARP. We created an ecological niche model for India using vegetation and topographic data and further refined it by including 18 additional bioclimatic data sets. Based on the ecological niche modelling results, a gap analysis of protection offered to potential Fox habitat in two states of southern India was conducted by overlaying existing protected area boundaries on the refined distribution and calculating the extent of protection. Our analysis showed that the Indian Fox habitat consists primarily of low elevation semi arid grassland, scrub and thom forests, which rank among the most velnerable in India owing to conversion to agriculture, industry and urban areas. The gap analysis showed that a little over 1% of predicted Fox distribution is covered by the protected area network. The under representation of these habitats is deleterious not only to the Indian Fox but also to a range of other species, such as the endangered Great Indian Bustard, Indian Grey Wolf and Blackbuck.