We utilize empirically derived estimates of landscape resistance to assess current landscape connectivity of American marten (Martes americana) in the northern Rocky Mountains, USA, and project how a warming climate may affect landscape resistance and population connectivity in the future. We evaluate the influences of five potential future temperature scenarios involving different degrees of warming. We use resistant kernel dispersal models to assess population connectivity based on full occupancy of suitable habitat in each of these hypothetical future resistance layers. We use the CDPOP model to simulate gene exchange among individual martens in each of these hypothetical future climates. We evaluate: (1) changes in the extent, connectivity and pattern of marten habitat, (2) changes in allelic richness and expected heterozygosity, and (3) changes in the range of significant positive genetic correlation within the northern Idaho marten population under each future scenario. We found that even moderate warming scenarios resulted in very large reductions in population connectivity. Calculation of genetic correlograms for each scenario indicates that climate driven changes in landscape connectivity results in decreasing range of genetic correlation, indicating more isolated and smaller genetic neighborhoods. These, in turn, resulted in substantial loss of allelic richness and reductions in expected heterozygosity. In the U.S. northern Rocky Mountains, climate change may extensively fragment marten populations to a degree that strongly reduces genetic diversity. Our results demonstrate that for species, such as the American marten, whose population connectivity is highly tied to climatic gradients, expected climate change can result in profound changes in the extent, pattern, connectivity and gene flow of populations.