Intercropping fennel (Foeniculum vulgare Mill.) with naturally colored cotton (Gossypium hirsutum L.) may provide a beneficial socioeconomic, ecological and environmental alternative for recuperating agribusiness in fennel and cotton cultivations in northeast Brazil because these crops do not compete for nutrients. The objectives of this study were to investigate the vertical and horizontal distribution of Hyadaphis foeniculi (Pass.) within fennel plants and its population dynamics in fennel crops and fennel intercropped with naturally colored cotton as a function of plant age during 2 fennel seasons by examining plants throughout the entire growing seasons. The vertical and horizontal distributions and the dynamics of the fennel aphids on the monocultured fennel and fennel intercropped with cotton were determined at intervals of 7 days, sampling 5 whole plants per plot from 55 days after transplanting the fennel seedlings until the first harvest (195 days after transplanting). The vertical distribution of apterous or alate aphids on the fennel plants evidenced no significant interactions within the cropping system, plant age, or vertical region of the plant, or between the cropping system and the vertical region of the plant. However for the number of fennel aphids per plant, there was an interaction between cropping system and plant age (apterous aphids) and between plant age and vertical region of the plant (apterous or alate aphids). In the fennel system, the apterous aphid population peaked at 153 and 188 days after transplanting, whereas the alate aphid population peaked at 139 and 174 days after transplanting. In the intercropped fennel/cotton system, the apterous aphid population peaked at 188 days after transplanting, and the alate aphid population peaked at 195 days after transplanting. The numbers of apterous aphids found per fennel plant in the monocultured fennel for the entire study were significantly higher than the numbers found in the fennel-cotton intercropped system. The results of our study are extremely important for understanding the vertical and horizontal distribution of H. foeniculi on fennel plants in both monoculture and the fennel-cotton intercropping system and may be useful in decision-making in relation to implementing controls and determining the timing of population peaks of this important fennel pest.