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Recent declines in large herbivores have led to significant conservation efforts globally. However, the niche-specific megaherbivores residing outside protected areas face more imminent extinction threats. Swamp deer, the obligate grassland-dwelling endemic cervid is the most extinction-prone megaherbivore in the Indian subcontinent. Limited information on distribution and habitat status pose significant conservation and management challenges for the remaining fragmented populations in north, north-east and central India. To this end, we combined exhaustive field surveys and Maximum Entropy (MaxEnt) modeling to generate the most detailed distribution map for the northern swamp deer subspecies. We used primary data from more than 6000 km2 field surveys and eight ecologically relevant covariates for model predictions. Grassland cover, annual mean temperature and distance from water were the major factors that predicted the species distribution. Models predicted swamp deer distribution in only ~3% of the entire landscape, covering both protected (~1.4%) as well as non-protected (~1.6%) areas. Our validation surveys in some of these predicted areas confirmed swamp deer presence and indicated ~85% model accuracy. Finally, we identified four ‘Priority Conservation Areas’ still retaining adequate grassland habitat and species presence that require immediate attention to ensure population connectivity across this landscape. These results highlight the importance of the marginalized grassland ecosystems of northern India that still retains high biodiversity. We suggest a swamp deer-centric conservation approach to protect these human-dominated habitats and emphasize in generating such information for other endemic, habitat-specialist species across the globe.