Habitat loss and fragmentation are among the major causes of the loss of terrestrial biodiversity. In particular, the tropical regions of the world are affected by these processes. The presented study examines the effects of habitat fragmentation and isolation on three selected autochthonous leaf-litter frog species of the Brazilian Atlantic Forest, which is extremely threatened by habitat fragmentation. Population dynamics and morphology of a generalist species (Chaunus ornatus), a species of intermediate habitat specialisation (Eleutherodactylus guentheri), and a specialist species (Eleutherodactylus parvus) have been studied. The results show unexpected positive response to habitat fragmentation of the highly specialised species of the genus Eleutherodactylus. The specialist species was captured only in isolated forest fragments and showed high survival probabilities and population sizes in these areas. The species of intermediate habitat specialisation showed tendential higher abundances and population sizes and significantly higher survival rates in the fragmented area compared to the unfragmented control. Significant differences in morphological parameters between study sites were not found for this species. The generalist species partly showed the expected negative response on habitat fragmentation. Significant lower values in morphological parameters in an isolated fragment compared to the unfragmented control were found for this species. Possible reasons for the response of the studied species are discussed and conclusions for the conservation value of the results are given.