Studies on the effects of nonindigenous invasive species and habitat fragmentation on native ecosystems have become priorities for conservation biologists. This is relevant particularly for islands with high degrees of endemism. In the present paper the role of fragmentation and possible effects of introduced Rattus rattus on endemic rodents (Macrotarsomys bastardi and Eliurus spp.) and the gray mouse lemur (Microcebus murinus) were assessed for dry deciduous forests in Madagascar. Capture rates of endemic rodents declined significantly with declining fragment size. Macrotarsomys bastardi was never caught in primary forest fragments < 600 ha or outside the primary forest but captures of M. bastardi were correlated to changes in vegetation structure associated with fragmentation rather than to fragment size per se. Eliurus spp. were also found in small primary-forest fragments and in secondary forests close to primary forests, suggesting that secondary forests can serve as buffer zones or corridors for this species. The lemur M. murinus was caught in all types of primary and secondary forest. This species did not seem to respond to fragmentation of primary forests. Even though it was found in most secondary-forests, capture rates declined as these secondary forest formations increased in size. This indicates that secondary forests are suboptimal habitats for M. murinus. Rattus rattus were caught in all vegetation formations except for the open savanna. Their capture rates increased as forest fragments became smaller, indicating that mosaics of different habitat types are beneficial for introduced rats. There was no significant relation between capture rates of R. rattus and the endemic species. In conclusion, these results suggest that (1) native Malagasy rodents of the dry deciduous forest are more sensitive towards forest disturbance than M. murinus; (2) there is no indication for negative interactions between introduced rats and the native small-mammal fauna.