Mass drug administration (MDA) with praziquantel is the cornerstone of schistosomiasis control and elimination efforts. To assess how long-term MDA affects parasite populations, we analyzed whole-genome sequence data from 570 Schistosoma mansoni samples and the closely related Schistosoma rodhaini across eight countries, combining new parasite material with publicly available sequence data. We observed a broad-scale genetic structure between countries alongside evidence of extensive long-distance transmission. Functional profiling of the recently identified transient receptor potential melastatin ion channel, Sm. TRPM PZQ , revealed four naturally occurring variants associated with reduced praziquantel sensitivity, indicating standing variation for resistance. Analyses of parasite infrapopulations collected from people pre– and post–praziquantel treatment further identified instances of treatment failure, supporting the potential for praziquantel resistance. As schistosomiasis is targeted for elimination as a public health problem, with interruption of transmission in selected regions by 2030, our study provides a comprehensive genomic framework for endemic populations, highlights an approach to detect potential resistance, and endorses the development of precision surveillance and adaptive treatment strategies.