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Abstract In Kenya, communities residing along the shores and islands of Lake Victoria bear a substantial burden of schistosomiasis. Although there is a school-based deworming program in place, the transmission of Schistosoma mansoni varies even at a fine scale. Given the focal nature of schistosomes’ transmission, we aim to identify areas with high intensity of S. mansoni infection in Mbita, Homabay County, western Kenya, for prioritized integrated control measures. Our findings confirm a high intensity of S. mansoni infection cluster around Mbita causeway. While the current efforts to curtail morbidity due to schistosomiasis through preventive chemotherapy in schools are crucial, fine-scale mapping of risk areas is necessary for specific integrated control measures.