We describe the vertical and horizontal distribution of the cotton aphid Aphis gossypii Glover within a cotton plant in two cotton (Gossypium hirsutum Linnaeus) cultivars (BRS Safira and BRS Rubí) with colored fiber over the time. Measurements of aphid population dynamics and distribution in the cotton plants were recorded in intervals of seven days. The number of apterous or alate aphids and their specific locations were recorded, using as a reference point the location of nodes on the mainstem of the plant and also those on the leaves present on branches and fruit structures. The number of apterous aphids found on the cultivar BRS Safira (56,515 aphids) was greater than that found on BRS Rubí (50,537 aphids). There was no significant difference between the number of alate aphids found on the cultivars BRS Safira (365 aphids/plant) and BRS Rubí (477 aphids/plant). There were interactions between cotton cultivar and plant age, between plant region and plant age, and between cultivar and plant region for apterous aphids. The results of this study are of great importance in improving control strategies for A. gossypii in the naturally-colored cotton cultivars BRS Safira and BRS Rubí.