1 Spatial and temporal habitat heterogeneity represented by annual crops is a major factor influencing population dynamics of phytophagous insect pests such as the cotton aphid Aphis gossypii Glover. We studied the effects of instability of the cotton agroecosystem resulting from the temporary availability of the plant resource and the repeated use of insecticides on the genetic variability of the cotton aphids. 2 Samples of A. gossypii were collected in cotton plots, treated or not with insecticides and from vegetable crops (Malvaceae, Cucurbitaceae and Solanaceae) within the cotton growing area of northern Cameroon. The genetic structure of the samples was assessed using eight microsatellite markers. Insecticide resistance was estimated through the detection of two mutations in the ace -1 gene that are associated with insensitivity of acetylcholinesterase to carbamate and organophosphate insecticides. 3 The results obtained show that both host plants and insecticides act in genetic structuring of A. gossypii . Ninety-three percent of aphids collected on cotton were characterized by the same microsatellite multilocus genotype, Burk1 , which also displays the insecticide resistant alleles. 4 During the dry season, the cotton crop season after, the genotype Burk1 was principally found on two other malvaceous cultivated plants, rosella and okra, acting as suitable reservoir plants. The ability of the cotton aphid to move among asynchronous suitable habitats in response to changes in resource availability enables the pest to exploit unstable cropping systems. An understanding of the cotton aphid life system may aid to improve strategies for integrated resistance management.Keywords Agricultural landscape , Aphis gossypii , cotton , genetic diversity , host plant specialization , insecticide resistance , microsatellite markers . offspring of immigrant insects is strongly affected by cultural practices, particularly insecticide use ( Kennedy & Storer, 2000 ).In sub-Saharan west and central Africa, cotton fields occupy a significant part of the agricultural landscape during the rainy growing season (mid-May to November) and harbour a great diversity of insect pest species whose populations are partially controlled by the use of insecticides ( Renou & Deguine, 1992 ). The dry season involves a rapid change in this agricultural landscape, with a sudden shortage of resources for phytophagous insects. At this time, small irrigated plots generally located in the vicinity of towns and villages probably play a key role in the life systems of cotton insect pests. The cotton aphid Aphis gossypii Glover is a cosmopolitan and polyphagous species widely distributed in tropical, subtropical and temperate regions. In west and central Africa, this aphid colonizes cotton crops from mid-July to November, whereas small surfaces of irrigated vegetable crops and opportunist weeds are mainly infested by A. gossypii from November to late April ( Deguine et al. , 1999 ). Two periods of population growth on cotton crops are generall...