The population structure of the malaria vector Anopheles arabiensis was investigated using data from six microsatellite loci in samples from localities in Mozambique and Tanzania. Genotype frequencies were neither significantly different between houses in a village in Tanzania nor between villages within a 20-km radius in Mozambique. Thus a deme has an area greater than 20 km in radius. At five of the six loci the heterozygosity of the population from Mozambique was lower than that from Tanzania, implying a lower effective population size (Ne) at this southern edge of the species range. There were significant differences in genotype frequencies between the Tanzanian and Mozambique populations at five of the six loci (P<0.05). Values for both FST (mean=0.069) and RST (mean=0.025) were significantly different from zero (P<0.05) at four and three out of five loci, respectively, but there was no significant correlation between the two statistics. The wide variation in values of FST and RST across loci suggests that care should be taken in interpreting values derived from averaging across loci. Whether the variation results from sampling effects or selectional constraints on some loci is unclear. Although there is evidence for significant differentiation between these populations, estimates of gene flow (Nm) calculated from mean FST and RST statistics were relatively high, 3.4 and 4.9, respectively. We argue that this is more likely to reflect recent separation of these populations and/or large effective population size rather than large-scale present day migrations.