The freshwater snail Biomphalaria pfeifferi is the main intermediate host of human intestinal Bilharziasis. It is widely distributed in Africa, Madagascar and middle-eastern countries, and its habitat includes wetlands, and arid to semi-arid areas. Based on analysis of 18 microsatellites, we investigated reference allelic variation among 30 populations of B. pfeifferi from three drainage basins in Dhofar, Oman (the eastern limit of its distribution). This is an arid to semi-arid region, with a 9,000-year history of very low rainfall, but is subject to unpredictable and destructive flash floods. In this context we showed that genetic fixation was very high compared to genetic differentiation which was moderate and, that, relative to B. pfeifferi populations from wetlands, the populations in Dhofar show evidence of lower levels of genetic diversity, a higher degree of genetic fixation, a quasi-absence of migration, and a higher level of genetic drift. Despite the extreme conditions in the Dhofar habitat of this species, it is able to survive because of its very high self-fertilization (approaching 100 %) and fecundity rates.