Relative diversity within and between small mammal assemblages of riparian and upland vegetation was evaluated at 6 study areas across an elevational gradient. In contrast to avian diversity analyses conducted at the same sites, species richness, relative diversity, and faunal similarity of small mammals were greater among upland rather than riparian communities across the cline. Beta diversity between riparian and upland small mammal communities is greater at higher elevations within the watershed. These higher elevation portions of watersheds must be emphasized in management strategies to conserve regional integrity of native small mammal faunas.