Schistosomiasis is a tropical neglected disease commonly associated with rural areas; however, urban schistosomiasis has been reported world-wide, and increasing urbanization is one of the most important demographic shifts of the 20 ^th and now 21 ^st centuries. The pattern of urbanization is not uniform so that within the same city the rates and sources of population increase vary. Here we report on the parasite composition in one neighborhood in the metropolitan area of Salvador, Bahia, Brazil. Using epidemiological data and population genetics we find evidence for local transmission and maintenance of Schistosoma mansoni infection within an urban population and little contribution from rural-urban migration. Our findings provide direction for local mitigation strategies and to assist the public living in this neighborhood to interrupt the local transmission cycle.