The objective of this study is to characterize the risk of flooding in the Agro zone 5 of Benin. The methodological approach can be summarized in several stages: the determination of the various climatic extreme indices (Rx1day, R95p and R99p) obtained by the rain data from the stations of Bohicon, Save and Parakou, then the analysis of the occurrence of these indices is made by the frequency analysis method, and finally the mapping of areas at risk of flooding is carried out based on the geological funds, the Digital Terrain Model (DTM), the land use units and rainfall data at the various stations covering the study area. The identification of areas at risk of flooding is governed by the combination of thematic maps based on the multi-criteria analysis method. The vulnerability map is obtained thanks to three physical factors which are: the slope, the drainage density and the geological units. The hazard map is obtained by combining land cover and rain fields. The results of this research reveal that in the Agro zone 5 of Benin, daily maximum rainfall of 60.68mm and 126.43mm has a probability of 0.5% and 0.2% of occurring for return periods of 2 and 5 years. The combination of the vulnerability and flood risk map shows that high and very high flood risk areas cover 24% of the total area of the study area.