Mastomys natalensis is the major pest rodent in sub-Saharan Africa. In this study, population genetic techniques were used to gain new insights into its dispersal behaviour, a critical parameter in pest management. Using 11 microsatellites, 272 individuals from a 300 ha area in Tanzania were genotyped. Genetic diversity was high, with no isolation by distance and little differentiation between field plots far apart, indicating a large effective population size and high dispersal rates in agreement with ecological observations. On the other hand, genetic differentiation between nearby field plots, isolation by distance within a single field plot and kin clustering were also observed. This apparent contradiction may be explained by yearly founder effects of a small number of breeding individuals per square area, which is consistent with the presence of linkage disequilibrium. An alternative, not mutually exclusive explanation is that there are both dispersing and sedentary animals in the population. The low-density field plots were characterized by low relatedness and small genetic distances to other field plots, indicating a high turnover rate and negative density-dependent dispersal. In one field plot female-biased dispersal was observed, which may be related to inbreeding avoidance or female competition for resources. Most juveniles appeared to be local recruits, but they did not seem to stay in their native area for more than two months. Finally, possible implications for pest management are discussed.