A sodium channel ‘kdr’-type mutation was identified in the M form of Anopheles gambiae from Burkina Faso in the tropical savannah area belt. The molecular M form of An. gambiae is found at high frequencies in the flooded rice cultivation area of Kou Valley, where the insecticide selection pressure is limited. The spread of the mutation in the M population is an ongoing process, as it increased from a frequency of 0.006 in 1999 to 0.02 in 2000. The S molecular form occurs in sympatry in our study village, with the M form at a relatively low frequency. The common ‘kdr’ mutation was previously detected in this area in the S form, and has probably invaded the M population through genetic introgression. This impacts on the question of actual levels of gene flow between the two molecular forms in tropical savannah areas. A hybrid M/S individual was identified during the course of this study, which was homozygous for the ‘kdr’ mutation. Pyrethroid resistant An. gambiae were caught in October and November, which is the time of year that the molecular S form migrates into this area as rain-fed breeding sites in the cotton fields dry out.