Exploratory human activities have resulted in small fragments inserted into a matrix which is inhospitable to small non-flying mammals. The effects of landscape changes alter the distribution patterns of species. Landscape fragmentation patterns for small mammals are controversial, especially considering small fragments and ecotonal regions. Based on these arguments, we investigated the diversity patterns of small mammals in small fragments in the ecotonal Cerrado/Atlantic Forest region. A total of 24 fragments (<40 ha) were studied using tomahawk, sherman and pitfall traps. We found low species richness (11 species, six marsupials and five rodents), which was not expected because it is an ecotonal region. It was verified that composition and community structure are simplified by the marked presence of generalist species and with the increase of species turnover. The small forest fragments present a microhabitat structure with lianas and streams as main environmental filters of groups with ecological similarities. Our findings suggest that these fragments must be managed in order to conserve the local biodiversity and maintain the needed characteristics to enable the occurrence of different ecological groups.