The small mammal species were investigated in the urbanized environment of Nitra city (Slovakia) in a multiscale-approach: at habitat level and at landscape level (urban-rural gradient). Continuous comprehensive rodent samplings from 2012 to 2015 were conducted in ten study sites, classified into three urban zones (landscape level). The total effort comprised 1,250 specimens of 13 species (Microtus arvalis, Apodemus sylvaticus, A. flavicollis, A. uralensis, Clethrionomys (Myodes) glareolus, M. subterraneus, Micromys minutes, Mus spicilegus, M. musculus, Crocidura suaveolens, C. leucodon, Sorex araneus, S. minutus) gathered in 14950 trapxnights. Environmental variables (habitat level) at each site were processed in the Geographical Information System as a proportion of landscape units around the trapping line and by a phytosociological survey. At the habitat level, we found a relationship between the landscape habitat structure and each species of small mammals. Diversity, species richness and relative abundance of small mammals decreased with the density of the built-up area. At landscape level, urban zones had a significant influence on species diversity, richness and relative abundance of small mammal populations. On the other hand, the presence of small mammal species precisely determined the urban zones, where we identified seven indicative species.