Small mammals should be considered in wildlife management decisions because they are an important component of ecosystems. We examined small mammal population abundances (N) on 4 habitat treatment types in Colorado pinyon pine (Pinus edulis)—Utah juniper (Juniperus osteosperma) woodlands on the Uncompahgre Plateau, Montrose, Colorado. We trapped small mammals in Sherman live traps on 4 habitat treatment types—including 2 types of management treatments (chaining, roller chop), sites with high drought-related mortality of pinyon pine, and sites of mature pinyon-juniper (PJ) woodland—on 3 mesas. We modeled detection probability of deer mice (Peromyscus maniculatus) and least chipmunks (Tamias minimus) as a function of 4 treatment types on 3 mesas during 2 trapping periods by using Huggins closed mark-recapture models. A variance components analysis was conducted to obtain abundance shrinkage estimates and to separate spatial process variance from the sampling variance to calculate the percent of variation in abundance estimates explained by treatment type, mesa, and trapping period. Abundance estimates were higher for deer mice and least chipmunks on chaining and roller chop treatment sites than on mature PJ woodland and pinyon pine natural mortality sites. The highest percent of variation in abundance estimates was explained by treatment type for deer mice (33.67%) and least chipmunks (61.45%) and secondarily by mesa for deer mice (21.64%). We calculated species diversity using Shannon's, Simpson's, Pielou's evenness, and species richness indices, and we used analysis of variance to test for significant differences (P < 0.05) in species composition. Species diversity and richness were higher on natural mortality sites than on chaining, roller chop, and mature woodland sites. Our results indicate that chaining and roller chop habitat treatments within PJ woodlands have a positive impact on deer mouse and least chipmunk abundances, whereas natural mortality and chaining treatments have a positive impact on small mammal composition.