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Townsend’s ground squirrels (Spermophilus townsendii) are important prey for raptors and other predators in the Snake River Birds of Prey Area in southwestern Idaho, an area undergoing drastic vegetation changes induced by fire. We used 54 transects of burrow entrances done in 1982 and recensused in 1986-1989 to determine how the vegetation changes were affecting squirrel populations and if Townsend’s ground squirrels will continue to provide a stable prey base for these predators. The mean number of active burrow entrances/ha decreased from 194 in 1982 to 68 in 1988. Burrow densities were highest and had the lowest annual variation in winterfat (Ceratoides lanata)-Sandberg’s bluegrass (Poa secunda) communities. Big sagebrush (Artemisia tridentata)-dominated communities had intermediate burrow densities, whereas shadscale (Atriplex confertifolia) communities had the lowest burrow densities. Burrow densities were highly variable in exotic annual communities, and negatively correlated with cheatgrass (Bromus tectorum) and other exotic annuals in all communities. Widespread conversion of desert shrublands to exotic annual-dominated communities by wildfires appears to be creating an increasingly unstable prey base for raptors in the Snake River Birds of Prey Area.