Tropical forest mammal assemblages are widely affected by the twin effects of habitat loss and habitat fragmentation. We evaluated the effects of forest patch metrics, habitat structure, age of patch isolation, and landscape metrics on the species richness, abundance and composition of small mammals at 23 forest fragments (ranging in size from 43 to 7,035 ha) in a highly deforested 3,609-km2 landscape of southwestern Brazilian Amazonia. Using pitfall traps and both terrestrial and arboreal traplines of Sherman, Tomahawk and snap traps, we captured a total of 844 individuals over 34,900 trap-nights representing 26 species and 20 genera of small-mammals, including 13 rodent and 13 marsupial species. We also consider the effects of distance from forest edges on species occupancy and abundance. Overall small mammal abundance, species richness and species composition were primarily affected by the quality of the open-habitat matrix of cattle pastures, rather than by patch metrics such as fragment size. Ultimately, small mammal community structure was determined by a combination of both landscape- and patch-scale variables. Knowledge of the anthropogenic factors that govern small mammal community structure is of critical importance for managing the persistence of forest vertebrates in increasingly fragmented neotropical forest landscapes.