Current evolutionary forces and historical processes interact to shape the distribution of neutral genetic variability within and among populations. Focusing on the genetics of recently introduced organisms offers a good opportunity to understand the relative importance of these factors. This study concerns variation at 8 polymorphic microsatellite loci in 30 populations of Biomphalaria pfeifferi. The sampling area spans most of the species’ range in Madagascar where it was probably introduced recently. Extremely low variation was found within all populations studied, which may partly result from high selfing rates. However, this cannot account for the variance of variation across populations, which is better explained by habitat openness (that reflects environmental stochasticity), the prevalence of the parasitic trematode Schistosoma mansoni and historical demography (colonization and subsequent bottlenecks). Large global differentiation was also observed, suggesting that current gene flow among populations is limited to small distances, within watersheds and to few individuals. Our data set also allowed us to test several hypotheses regarding colonization, based on bottleneck and admixture tests. The observed pattern requires at least two independent introductions from slightly differentiated genetic sources in the western part of Madagascar. Another introduction, from a very different genetic origin, should also be postulated to explain the genetic composition of eastern populations. That this introduction occurred recently suggests that the colonization of Madagascar by B. pfeifferi is an ongoing process.