Population connectivity is a function of the dispersal ability of the species, influences of different landscape elements on its movement behavior, density and distribution of the population, and structure of the landscape. Often, researchers have not carefully considered each of these factors when evaluating connectivity and making conservation recommendations. We present a general method for efficient evaluation of functional connectivity for large numbers of native species across vast geographical areas. Connectivity was evaluated for 36 groups of species with different ecological associations; within each of these groups, three dispersal abilities were evaluated across the United States northern Rocky Mountains. We quantified the extent and fragmentation of predicted connected habitat for each of these 108 species and identify those for which the current landscape has the lowest area and the highest fragmentation of habitat. We then conducted a multivariate ordination and use landscape trajectory analysis to assess multivariate differences in the extent and fragmentation of connected habitat across taxa. We mapped habitat connectivity for each of the 108 species, quantified the extent and pattern of connected habitat for each species, identified which species have the most limited extent and most highly fragmented pattern of connected habitat, identified any groups of species with similar patterns of connected habitat across dispersal abilities, and quantified the sensitivity to landscape pattern of connected habitat to dispersal ability and different ecological associations. We found large differences among groups of species in terms of the extent and connectivity of habitat, and the sensitivity of connectivity to dispersal ability. Species with limited dispersal ability associated with low-elevation forest have the most limited and fragmented distribution of connected habitat. Species associated with high-elevation forest also appear highly vulnerable to habitat loss and fragmentation based on limited extents and connectivity of habitat.