The cotton aphid Aphis gossypii Glover is key pest of cotton in northern Cameroon, particularly at early crop stages. The objective of this work was to evaluate the clonal diversity and host specificity of aphids' populations infesting cotton. To accomplish this task, samples were collected at different periods, in different sites and from different host plants in the cotton-growing area of Cameroon. The genetic structure of collected samples was screened using microsatellite markers while demographic parameters of cotton aphids according to host plant were assessed in laboratory bioassays. Very low clonal diversity was observed in A. gossypii populations, as only three clones were detected in the samples originating from cotton. During the dry season, the major clone (Burk) was found principally in cultivated malvaceous plants such as roselle and okra that constitute excellent relay host plants. In addition, the intrinsic rate of population growth (r.) of this clone was found to be equal on okra (0.32) but significantly greater on roselle (0.42), compared to cotton. On the contrary, Burk was rarely found in aphid colonies collected from Cucurbitaceae and Solanaceae, and antibiosis tests confirmed that reproductive potential was negatively affected on melon (0.22) and sweet pepper (0.00). These results confirm that host plant specificity acts in genetic structuring of aphid populations, with particular emphasis on cotton aphids.