An exceptionally high degree of biodiversity and endemic species is concentrated in the tropical forests of Southeast Asia. Large-scale anthropogenic deforestation in this region resulted in habitat loss and fragmentation, and causes severe problems for the maintenance of the biodiversity. Effects of habitat fragmentation have been studied comprehensively, but negative consequences are still controversially discussed and cannot be generalised. One reason is that the impacts of habitat fragmentation depend on several species-specific traits, and individuals of different species can be affected in a variety of ways. Knowledge of the ecological plasticity and sensitivity of a wide range of species is therefore essential to evaluate generalised fragmentation effects and to formulate effective conservation and management plans. Tropical small mammals, which occur in highly diverse and species-rich communities, are a suitable model to assess fragmentation effects on species with varying ecological requirements. This thesis investigated population genetic structures in non-volant small mammal communities inhabiting forest fragments in the Lower Kinabatangan floodplain on Borneo. The landscape along the Lower Kinabatangan River is highly degraded by anthropogenic modifications and dominated by oil palm plantations but still retains a high floral and faunal diversity. The impact of landscape modifications has so far been studied for larger animals but not for small mammals of this region. Equally scarce are population genetic studies assessing the influence of the fragmented landscape on population genetic structures to evaluate long-term viability and population persistence. Until now, this has only been conducted for the Bornean elephant and some primate species. Furthermore, in fragmented habitats, biogeographical barriers, such as rivers, might represent an important additive factor restricting migratory capabilities even further, leading to a reduction or interruption of gene flow and an increased genetic ...