This paper addresses the ecosystem characteristics, biodiversity, conservation priorities, current threats and sustainable management of Khar Yamaat Nature Reserve, which lies in northeastern Mongolia. The formation of Khar Yamaat’s ecosystem and its biological diversity are unique in eastern Mongolia. Biogeographically, this nature reserve is located at the intersection between different phytogeographical regions, specifically the Central-Khalkh dry steppe, Mongol-Dahurian forest-steppe, and Eastern-Mongolian tall-grass steppe. As such, this nature reserve is home to a diverse complement of plants and animals representing the various ecoregions, was established in 1998 to protect 50,691 hectares of rocky-mountains surrounded by vast steppes. Khar Yamaat’s unique geological formation and assemblage of ecosystems have, since then, become an area of focus for environmental restoration and a center for research and monitoring. In general, the habitats of the nature reserve were found to be largely intact, if stressed to varying degrees, but wildlife populations appeared to be low. Anthropogenic influences, particularly heavy grazing by livestock, have threatened some species of vascular plants with extinction and reduced the abundance and distributions of a few other species. Serious threats included excessive or illegal take of plants and animals, overgrazing by livestock, human caused wildfires, climate change and associated drought, and mining in the buffer zone. In this paper, we discuss issues of conservation and sustainable management of Khar Yamaat Nature Reserve.