Cryptic species are phylogenetically diverged taxa that are morphologically indistinguishable and may differ in their ecological and behavioral requirements. This may have important implications for ecosystem services and conservation of biodiversity. We investigated whether two ecologically important cryptic species of the freshwater amphipod Gammarus fossarum (types A and B) are associated with different habitats. We collected data on their occurrence at both the landscape scale (large watersheds) and at the local scale (river reach) to compare macro-and microscale environmental parameters associated with their presence. Analysis of the landscape scale data showed that occurrence of types A and B differ with respect to watershed and river size and, interestingly, human impact on river ecomorphology. Whereas type B was mainly found in less forested areas with higher human impact, type A showed the opposite occurrence pattern. Analyses of the local scale data suggested that habitats occupied by type A were characterized by larger gravel, larger stones and less macrophytes than habitats occupied by type B. The landscape and local data set showed contradicting patterns with regard to stream size. Overall, the observed differences between the two types of G. fossarum most likely reflect ecological differences between them, but alternative explanations (e.g., historical colonization processes) cannot be completely ruled out. Our study underlines that common cryptic species can differ in their ecology and response to anthropogenic influence. Such differences in habitat requirements among difficult-to-identify taxa present a challenge for biodiversity and ecosystem management. Our results emphasize the importance of conservative and precautionary approaches in maintenance of habitat diversity and environmental heterogeneity.