OBJECTIVES: Schistosomiasis is an important disease in Madagascar, and several studies on the disease have focused on the occurrence of the parasite in humans. However, the range of the pathogen in the environment and its impact on human infection is difficult to predict. An environmental DNA (eDNA) detection system for Schistosoma mansoni was developed to improve schistosomiasis eco-epidemiology studies. METHODS: Primers and probes were designed and tested in experimental biotopes. The field study was conducted in Maevatanana District of Madagascar. Seven water sources with human use were sampled, with a total of 21 water samples collected. Snails were collected, and patients were examined by ultrasound to determine the occurrence of schistosomiasis in the study area. RESULTS: One water source with active transmission was identified through the detection of S. mansoni eDNA in the water and the intermediate host Biomphalaria pfeifferi collected from the same water source. People with clinical schistosomiasis were found in the area, reinforcing the findings. CONCLUSIONS: The application of eDNA in eco-epidemiology enables the determination of hot spots and safe spots in endemic areas, constituting an alternative ecological tool for follow-up and monitoring of control programs for schistosomiasis, and contributing information on water safety for improving the standard of living of the people in endemic areas.