Monitoring of the spread of insecticide resistance in field vector populations is a prerequisite for the implementation of efficient and sustainable vector control strategies based on the use of insecticides. Screening for resistance alleles in Anopheles gambiae populations is facilitated by the availability of molecular diagnostics to detect major target-site mutations, such as knock-down resistance (kdr) and insensitive acetylcholinesterase (ace-1R). Anopheles gambiae mosquitoes were collected resting indoors in two villages within a rice cultivation area in western Burkina Faso, from January to December 2007. Specimens were identified to species and molecular form and their genotype at the kdr and ace-1 locus was determined using PCR and RFLP protocols. The M form was largely predominant in our samples and was present all year round in both villages. S-form mosquitoes gradually appeared during the rainy season in the village at the margins of the rice fields (VK7) whereas it was very rare in the center of the rice cultivation area (VK5) throughout the survey. The frequency of both kdr and ace-1R mutations was higher in the S than in the M form at any time. In the M form, frequency of the kdr mutation was higher during the rainy season in both villages (P<0.005). We report occurrence of the ace-1R mutation in the M form, albeit at a low frequency (<1%). Our results highlight the preoccupying status of insecticide resistance in An. gambiae populations from Burkina Faso, and suggest that comprehensive monitoring strategies need to consider population dynamics. (Texte intégral)