Madagascar presents a large heterogeneity in terms of climate and altitude, which explains the uneven spread of malaria throughout the island. The capital, Antananarivo, counts more than one million inhabitants, altitude between 1250 and 1470 m, in an area where the transmission is low but malaria may cause deadly epidemic outbreaks. Numerous malaria cases are reported, without biological confirmation, and reliable data about urban malaria transmission are lacking. The " Institut Pasteur de Madagascar" together with the Malagasy Ministry of Health performed in 2003 a study about malaria transmission in Antananarivo. A prevalence survey of malaria among fever syndromes, with data collected from 43 urban dispensaries, showed that confirmed malaria cases represented only 2% of the total fever cases (15 cases out of 779 fever syndromes). The vast majority was imported from costal areas (13 cases out of 15), where malaria is hyperendemic. However, a local urban transmission was found for two patients and five other subjects identified during a proximity survey. Vectors A. arabiensis and A. funestus were found inside the patient houses, located in close proximity of flooded rice fields. Genetic analysis of P. falciparum strains allowed to distinguish three genotypes, aggregated by house. The analysis of parasite genome polymorphism proves here its validity for epidemic surveys in areas where malaria is unstable, with no premunition in the local urban population.