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Background In arid settings, droughts usually lead to periods of very low or no malaria transmission. However, in rural Kandi (Sonsoro) in northeastern Benin, several malaria cases are often diagnosed during dry seasons. The underlying factors accounting for this phenomenon remain unknown. Methods The entomological profile of Sonsoro has been studied compared to a location in urban Kandi (Gansosso) for a period of one year. During this period, Anopheles larval habitats were investigated and populations of Anopheles gambiae s.l. were sampled by human landing catches in both areas. Enzyme-linked immunosorbent assays (ELISA) for Plasmodium falciparum circumsporozoite protein (CSP) were conducted on vector specimens and the entomological inoculation rates (EIR) were determined per season (wet versus dry) in each area. In addition, during the severe drought period, Rapid Diagnostic Tests (RDTs) were conducted on school children under the age 10 years in these areas to provide a global view of drought-malaria prevalence and to perform a crossing with entomological data in Kandi. Results Overall, An. gambiae s.l. was particularly abundant in rural Kandi compared to the urban area with a significant decrease of vector density in both sites during the dry season. In this period, larval sampling data identified household water sources as potential breeding sites in urban and rural Kandi. We also observed a significant seasonal variation of the infectivity rate in both areas but for each period (season), the EIR was higher in the rural site than in the urban. Data of P. falciparum detection was the reflection of entomological findings. The droughtmalaria prevalence was 5.5 times higher in rural Kandi as compared to urban Kandi. The presence of a permanent water site and the low level of urbanization in rural Kandi were identified as a risk factor. Conclusion Our data showed a high level of malaria transmission in the municipality of Kandi. Household water source plays an important role in maintaining the breeding of anopheles larvae and the malaria transmission in Kandi. In rural settings, the proximity to permanent water sites could probably be the aggravating factor. [ABSTRACT FROM AUTHOR]