Malaria in Brazil is virtually restricted to the Amazon Region, where it has a heterogeneous geographic distribution. We reviewed secondary data in order to describe the regional and temporal distribution of 8018 malaria cases seen between 2003 and 2007 in Santa Isabel do Rio Negro, a municipality in the northwest Brazilian Amazon. A significant rise in malaria incidence, mainly in the Yanomami Indian reservation, was observed during this time. Anopheline breeding sites were also mapped and entomological data were obtained through the capture of larval and adult mosquitoes. Thirty-three potential breeding sites were identified in the urban and periurban areas, 28 of which were positive for anopheline larvae. Anopheles darlingi specimens were captured in both intra- and peridomicile locations in the urban areas. Demographic data were also assessed via a sectional survey, revealing that the majority of dwellings were vulnerable to mosquitoes. This study suggests that urban and periurban areas of this municipality are highly susceptible to epidemic malaria, which is endemic in the Yanomami Indian reservation near the city. In addition, transmission can be perpetuated autochthonously in the urban area, drawing attention to the continuous need for preventative measures such as controlling adult and aquatic stages of mosquitoes and improving housing.