1. Pest rodents remain key biotic constraints to cereal crops production in the East African region where they occur, especially in seasons of outbreaks. Despite that, Uganda has scant information on rodents as crop pests to guide effective management strategies. 2. A Capture-Mark-Recapture (CMR) technique was employed to establish the species composition and community structure of small rodents in a maize-based agro ecosystem. Trapping of small rodents was conducted in permanent fallow and cultivated fields, each category replicated twice making four grids. At each field, a 6060 m grid was measured and marked with permanent trapping points spaced at 1010 m, making a total of 49 trapping points/grids. Trapping was conducted monthly at 4 weeks interval for three consecutive days for two and half years using Sherman Live traps. 3. Eleven identified small rodent species and one insectivorous small mammal were recorded with Mastomys natalensis being the most dominant species (over 60.7%). Other species were Mus triton (16.1%), Aethomys hendei (6.7%), Lemniscomys zebra (5.2%), Lophuromys sikapusi (4.8%), Arvicanthis niloticus (0.9%), Gerbilliscus kempi (0.1%), Graphiurus murinus (0.1%), Steatomys parvus (0.1%), Dasymys incomtus (0.1%) and Grammomys dolichurus (0.1%). Spatially, species richness differed significantly (p = 0.0001) between the studied field habitats with significantly higher richness in fallow land compared to cultivated fields. 4. Temporally, total species richness and abundance showed a significant interaction effect over the months, years and fields of trapping with significantly (p = 0.001) higher abundances during months of wet seasons and in the first and third year of trapping. In terms of community structure, higher species diversity associated more with fallow field habitats but also with certain rare species found only in cultivated fields. 5. Synthesis and applications. Currently, management strategies can be designed to target the key pest species and the most vulnerable habitats.