To shed first light on caprine schistosomiasis and its zoonotic potential in Malawi, we conducted a molecular epidemiological investigation, sampling goats (n = 230) across three districts, using faecal miracidia hatching test. Molecular genotyping of miracidia later revealed the prevalence of Schistosoma mattheei to be 0.0 % in Nsanje District (n = 30), 16.7 % in Chikwawa District (n = 30) and 25.3 % in Mangochi District (n = 170). Notably, a miracidium of Schistosoma haematobium was observed from a single goat in Chikwawa. Inspection of carcasses (n = 51) at two local abattoirs in Mangochi District did not find any evidence of caprine schistosomiasis where only a single herd, at Mangochi 3, was infected. Here, despite sampling several other herds nearby, the prevalence was 87.7 % (n = 49), with an animal found excreting 1000 miracidia per 5 g of faeces. At this location, our praziquantel treatment (n = 14) and GPS animal tracking (n = 2) pilot sub-study compared two local goat herds over a three-month period. The daily foraging ranges across a 10 km2 area were recorded, alongside targeted schistosome surveillance within local freshwater intermediate snail hosts. Analysis of GPS data revealed only one herd (infected) to have regular daily water contact with Lake Malawi whereas the other herd (not infected) totally avoided the lake. One week after praziquantel treatment administered at 40 mg/kg, anthelminthic cure rate was 92.3 % while at three months approximately a third of treated animals were shedding schistosome miracidia. Cercariae from several field-caught snails locally were genotyped, inclusive of finding a Schistosoma haematobium-mattheei hybrid. Our findings reveal the focalized nature of caprine schistosomiasis, signposting a novel alert for S. haematobium transmission, and highlight where zoonotic transmission can be intense. To better address zoonotic spill-over from S. mattheei (and/or S. haematobium), the national control programme for schistosomiasis should formally develop targeted surveillance of caprine schistosomiasis and where appropriate, attempt an integrated One Health intervention in future.