Background: New active ingredients, mostly repurposed from the agricultural sector, are gradually being introduced into malaria vector control programs. Prior to scaling up novel insecticides, it is vital to assess if their use in agriculture has already selected mosquito populations with reduced susceptibility in some areas. The aim of the present study was to determine if the use of neonicotinoids in agricultural pest management could drive resistance to clothianidin - a neonicotinoid recently prequalified by WHO for indoor residual spraying. Methods: We carried out intensive sampling of Anopheles gambiae, An. coluzzii and Culex sp. larvae from a large suburban farm and from 4 surrounding locations belonging to the rural and urban ecosystems of Yaounde, Cameroon. Using WHO tube tests and CDC bottle bioassays, we tested the recommended diagnostic doses of clothianidin against field-collected populations using two laboratory strains as susceptible controls. We exposed adult mosquitoes to the insecticide for 1 h and monitored mortality rates for seven consecutive days. Results: An. coluzzii and Culex sp. mosquitoes were fully susceptible to clothianidin reaching 100% mortality by day 3. By contrast, An. gambiae populations revealed heterogeneous profiles ranging from susceptibility to strong resistance. Populations from the suburban farm, where neonicotinoids are routinely used, displayed the lowest mortality rate (46.5 % ± 5.65) and were capable of surviving 5X and 10X the diagnostic dose of clothianidin. When clothianidin was tested in combination with the synergist piperonyl butoxide, mortality of resistant populations increased from 46.5 % to 92.7 % implying that Cytochrome P450 enzymes play an integral role in the genetic mechanism underlying clothianidin resistance in An. gambiae. Conclusions: These findings show that small clusters of resistance to clothianidin may exist around farmlands where agricultural neonicotinoids are being used. Patches of intensive agriculture should be particularly monitored in indoor residual spraying target areas.