The population genetic structure of the freshwater snail, Biomphalaria glabrata, was assessed in the municipality of Virgem das Graças (Minas Gerais, Brazil), a schistosomiasis-endemic area. The seven microsatellite loci that were used to genotype 326 individuals from 17 collection sites within a 3-km radius revealed high genetic variability. However, we found a deficit of heterozygotes relative to Hardy–Weinberg expectations for most of the loci and in many collection sites, indicating a high level of inbreeding. This may be the result of founder effects and sib-mating. A high level of overall population genetic differentiation among B. glabrata collection sites suggested low gene flow at this relatively small spatial scale in this region. However, subsequent analyses also indicated that these patterns may also result from founder events and that an exchange of individuals between particular collection sites does exist. The isolation-by-distance correlation between collection sites of B. glabrata was found to be significant. However, only approximately 6% of the variance in FST was explained by geographic distances suggesting that there are other factors affecting genetic differentiation among these collection sites. It is likely that the current population genetic structure reflects patterns of both migration and founder events. Results from this study are important for understanding the potential for local adaptation between schistosomes and their snail hosts at this epidemiologically relevant scale.