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Background  Urbanization in African cities has major impact on malaria risk. Niamey, the capital of the Republic of Niger, is situated in the West African Sahel zone. The short rainy season and human activities linked with the Niger River influence mosquito abundance. This study aimed at deciphering the factors of distribution of urban malaria vectors in Niamey.    Methods  The distribution of mosquito aquatic stages was investigated monthly from December 2002 to November 2003, at up to 84 breeding sites, throughout Niamey. An exploratory analysis of association between mosquito abundance and environmental factors was performed by a Principal Component Analysis and confirmed by Kruskall–Wallis non-parametric test. To assess the relative importance of significant factors, models were built for  Anopheles  and Culicinae. In a second capture session, adult mosquitoes were collected weekly with pyrethrum sprays and CDC light-traps from June 2008 to June 2009 in two differentiated urban areas chosen after the study’s first step. Members of the  Anopheles gambiae  complex were genotyped and  Anopheles  females were tested for the presence of  Plasmodium falciparum  circumsporozoite antigens using ELISA.    Results  In 2003, 29 % of 8420 mosquitoes collected as aquatic stages were  Anopheles . They were significantly more likely to be found upstream, relatively close to the river and highly productive in ponds. These factors remained significant in regression and generalized linear models. The Culicinae were found significantly more likely close to the river, and in the main temporary affluent stream. In 2009,  Anopheles  specimens, including  Anopheles gambiae s.l.  (95 %), but also  Anopheles funestus  (0.6 %) accounted for 18 % of the adult mosquito fauna, with a large difference between the two sampled zones. Three members of the  An. gambiae  complex were found:  Anopheles arabiensis ,  Anopheles coluzzii , and  An. gambiae . Nineteen (1.3 %) out of 1467 females tested for  P. falciparum  antigen were found positive.    Conclusion  The study provides valuable update knowledge on malaria vector ecology and distribution in Niamey. The identification of spatial and environmental risk factors could pave the way to larval source management strategy and allow malaria vector control to focus on key zones for the benefit of the community.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-016-1352-0) contains supplementary material, which is available to authorized users.

Ecology of urban malaria vectors in Niamey, Republic of Niger