The persistence of malaria transmission in areas with very arid environmental conditions remains enigmatic. The present study investigated seasonal variation of mosquito species composition and Kdr and Ace-1 mutations in Anopheles gambiae s.l. in the very arid district of Kandi in North-eastern Benin.Adult mosquitoes were sampled over 1 year using both human landing catches (HLC) and pyrethrum spray catches in 4 villages belonging to 2 areas of different levels of aridity. The collections were carried out on a bi-monthly basis in the wet season, and once every month in the dry season to better capture the entomological situation in drought period. Females An. gambiae sl specimens were kept aside and analysed by PCR for species identification. Presence of kdr and Ace-1 mutations was also assessed in the An. gambiae s.l. collection.A total of 2,211 host-seeking mosquitoes belonging to 15 species were collected in the study area. An. gambiae s.l. was the most abundant species and represented 67% of the collection. Other Anopheles species were found at very low frequency among which An. funestus, An. pharoensis, An. broheri and An. coustani. Molecular species identification showed in dry season a significantly higher frequency of An. coluzzii over An. gambiae s. s. in both less dry (70% vs 29% with p < 0.001) and driest (70% vs 30% and p = 0.034) areas of the district of Kandi. In the rainy season, there was similar frequency of An. coluzzii and An. gambiae s. s. in the less arid area (53% vs 45%; p = 0.153), while An. coluzzii remained significantly predominant (62% vs 38%; p = 0.012) in the driest zone. The frequency of kdr mutation was significantly higher in dry season than in rainy season (93% vs 84%; p<0.001), while no Ace-1 mutation was detected in the collection.In the current context of climate change marked by increasingly high temperatures and longer droughts, suitable vector control should be designed taking into account characteristics of the vector population maintaining malaria transmission in such arid environmental conditions.