It is known that intercropping systems maintain biodiversity and control pest populations. The aim of this study was to describe the vertical and horizontal distribution of the cotton aphid, Aphis gossypii Glover, within the cotton plant (Gossypium hirsutum L.) in cotton with colored fibers and cotton-fennel (Foeniculum vulgare Miller) intercropping system over time, during two cotton seasons. Measurements of the aphid population's dynamics and distribution in the cotton plants were recorded at intervals of 7 d, from plant emergence until the appearance of the first open bolls. The number of aphids and their specific locations on the plant were recorded in relation to reference points (nodes on the plant's main stem as well as on leaves and fruit structures). The number of cotton aphids found on the cotton crop (11,444 cotton aphids) was significantly higher than the number found on the cotton-fennel intercrop (8,106). Considering the vertical distribution of cotton aphids on the plants, no significant interactions were observed among the crop system, plant age and plant region, between the crop system and plant age, or between the crop system and plant region. In the cotton system, aphid populations peaked between 74 and 95 d, whereas in the cotton-fennel intercropping system, aphid populations peaked between 74 and 102 d. The results obtained in this study could be useful in decision-making, implementing controls and determining the timing of population peaks of this aphid.