We sought to assess the effects of forest fragmentation, introduced Rattus rattus, exotic tree plantations and secondary vegetation on the endemic rodent Eliurus webbi (Nesomyinae) and the lemur Microcebus murinus in the littoral forests of southern Madagascar. For E. webbi the number of individuals caught, the body mass of males and the percentage of females in the population were positively correlated with the size of the forest fragments. Capture rates and population characteristics of the other two species were uncorrelated with fragment size. None of the endemic species was caught outside the native forest while R. rattus inhabited all vegetation formations except for a newly planted corridor of tree saplings. Capture rates of both endemic species were uncorrelated with the number of R. rattus caught at the same site and thus did not indicate replacement of native species by R. rattus. The study demonstrated negative effects of fragmentation on capture rates of E. webbi and changes in their population characteristics. Exotic tree plantations or secondary vegetation seem to represent unsuitable or marginal habitats for the endemic species.