Southern Mongolia is an important area for wildlife conservation, because several long-distance migratory ungulate species inhabit it, but mining development and new railroad construction are progressing. To assess habitat fragmentation by new railroad construction on wild ungulates, we evaluated habitat suitability and important environmental factors for Mongolian gazelles (Procapra gutturosa) in summer and winter by using tracking data for 8 gazelles and environmental variables from September 2013 to September 2014 and species distribution models. We made habitat suitability maps for Mongolian gazelles in a wider range with similar environmental conditions from 2007 to 2014 by applying the best models to the past environmental data of vegetation index (NDVI) and snow cover. Spatial distribution of habitat suitability in winter was largely changed between the years due to the large interannual fluctuation of spatial distribution of snow-cover duration. Interannual change of spatial distribution of habitat suitability in summer was relatively slight. In areas potentially fragmented by new railroad construction, areas with >0.5 habitat suitability index was only 0.1% in the severest winter (2009-10) and decreased 99% from the former winter (2008-09). The drastic reduction of suitable areas within the range in severe winters suggests a serious threat of habitat fragmentation for long-distance migratory ungulates and the necessity for conservation measures to allow access to wide ranges across new railroads for wild ungulates.