The cotton aphids Aphis gossypii Glover constitute one of the key pests of cotton in north Cameroon, particularly at early stage. The objective of this work was to evaluate genetic diversity of aphid populations in cotton systems and to confirm the host race structure. To accomplish this task, samples were collected at different periods, on different sites and host plants belonging to the Malvaceae, Cucurbitaceae and Solanaceae families. Genetic structure of collected samples was sorted using microsatellite markers. Moreover, demographic parameters of identified clones and host choice were assessed in laboratory bioassays. There was little genetic diversity of the cotton aphids in north Cameroon. In effect, only two specialized clones constitute the cotton aphids. An important point of application is the clear identification of the cotton aphids, fot the elaboration of new strategies of integrated pest management.