Nepal is rich in biodiversity due to variability in elevation from 67m to Mount Everest. Out of 20 protected areas, government of Nepal has established 11 protected areas in Himalayan region of the country. Information on habitat preference and distribution of most of the wildlife species is lacking due to lack of the scientific study about the habitats of the animals. Studies to explore the relation between more animals are very limited. Government of Nepal and others conservation partners are feeling difficulties to manage the wildlife in their natural habitat due to lack of scientific and reliable information on their habitats. Habitat overlap survey can be the best study to identify the relation between the two species so the conservation of one animal can benefit the other one. In this study we identify important habitat parameters and overlapped habitat of the red panda (red cat bear; Ailurus fulgens) and Asiatic black bear (Ursus thibetanus) by the help of Maximum Entropy (MaxEnt) modeling in the Makalu Barun National Park, Nepal. GPS points of the species occurrence were collected from field and environmental variables were extracted from freely available sources. We identified the topographical and anthropogenic variable as best predictor of the distribution of the both species. The study area covers the 644 km2 habitat of Asiatic black bear and 534 km2 habitats of red panda. The 440 km2 habitat of both species is overlapped, which is 82 % habitat of red panda and 68% of habitat of Asiatic black bear. Most of the habitats are located inside the Buffer Zone of the National Park so the effective conservation work should be focused inside the Buffer Zone for the conservation of both species.