In cotton-growing areas of Central Africa, timing of host crops and pest management practices in annual rainfed cropping systems result in a shifting mosaic of habitats that influence the dynamics and resistance of Helicoverpa armigera (Hübner) populations on spatial scales, both within and across seasons. From 2002 to 2006, regional and local resistance was monitored among cotton fields and among the major host plants of the bollworm. From 2002, pyrethroid resistance increased within and across cotton-growing seasons to reach a worrying situation at the end of the 2005 growing season. Cotton crops played a fundamental role in the increase in seasonal resistance, even if the intensive use of insecticides on local tomato crops strongly concentrated resistance alleles in residual populations throughout the off-season. Due to the relative stability of resistance in H. armigera populations despite a long off-season, we believe that after the dispersal of the moths southwards at the end of the growing season, reverse migration mainly accounts for the reconstitution of populations at the onset of the following growing season. In addition, local resistance monitoring in 2005 and 2006 showed that it was possible to control the increase in resistance by temporarily stopping the use of pyrethroids during the period of peak infestation of cotton by H. armigera. On the other hand, the similar resistance frequency of populations sampled from sprayed and unsprayed synchronous hosts confirmed the absence of reproductive isolation between adults. As a result, diversity in cropping systems should be encouraged by planting alternative host plants to provide a mosaic of habitats, which in return would provide insecticide-free refuges. The implications for insecticide resistance management in annual cropping systems are discussed.