We studied the proportion of malaria-infected patients among febrile outpatients in nine health centres selected in relation to their geo-climatic location and the level of malaria transmission in order to establish a reliable database on malaria-associated morbidity and Plasmodium species in three epidemiological strata in Mauritania. Blood samples were collected from a total of 7368 febrile individuals (1603 in sahelian zone, 3023 in sahelian-saharan transition zone, and 2742 in Saharan zone) to examine thin and thick blood smears between August 2010 and July 2011. The proportion of malaria-infected patients was 9.1% (672/7368). Depending on the season, the proportion varied from 16.3% (494/3021), 5.5% (157/2850), to 1.4% (21/1497) during the humid season (July-October), cool dry season (December-March), and hot dry season (April-June), respectively. Febrile patients in the sahelian-Saharan transition zone were most affected by malaria, with 65.6% (441/672) smear-positive cases. P. vivax occurred most frequently (61.6%, 414/672). P. falciparum, P. ovale, and P. malariae accounted for 32.4% (218/672), 5.2% (35/672), and 0.8% (5/672) of smear-positive cases, respectively. These data may contribute to improving our knowledge on malaria in Mauritania, which may in turn help develop control strategies and improved monitoring in each geo-climatic zone.