In Sub‐Saharan Africa, Anopheles gambiae Giles (Diptera: Culicidae) largely contributes to malaria transmission, in direct relation to environmental conditions influencing the vector ecology. Therefore, we carried out a proteomic analysis on An. gambiae sensu lato (s.l.) mosquitoes to compare their metabolic state, depending on different pesticide pressures by selecting areas with or without cotton crops, in two climatic regions. Adult mosquitoes were collected, and the proteomes were analysed by liquid chromatography with tandem mass spectrometry (LC‐MS/MS).