Wildfires are becoming more prevalent in montane conifer forests of the San Bernardino Mountains of southern California. The effects of fire on stand structure and composition of these forests has been extensively studied but there are far fewer studies on how wildfires affect the fauna. For five years after a wildfire in 2007, we live-trapped small mammals in three burn types: unburned, moderate-severity and high-severity. A primary objective of this study was to document the response of the small mammal community to high-severity fire. Pinyon mice were consistently more abundant in unburned forests and declined by 69–76% between unburned forests and moderate-severity and high-severity burns. In contrast, deer mice responded positively to fire. Their numbers increased by 72%–87% between unburned forests and moderate-severity and high-severity burns. Compared to unburned forests, chipmunk numbers were 43%–64% lower in moderate and high-severity burns. California ground squirrels were unaffected by either severity. Using ordination analysis, we examined the distributions of the four small mammal species in relationship to stand structure and microhabitat variables that changed after fire. When the three burn types were analyzed together, small mammal composition was significantly related to burn type (unburned vs. high-severity), years-after-fire, litter cover and cover of bare ground. When the moderate and high-severity burn types were analyzed without unburned grids, four variables were significant: years-after-fire, rock outcrop cover, bare ground cover, and the combined covers of oak resprouts and shrubs.