A 2-yr study in cotton (Gossypium hirsutum L.) was conducted to determine the abundance and species composition of thrips (Thysanoptera: Thripidae) on different plant parts throughout the season in Alabama, Georgia, North Carolina, South Carolina, and Virginia. Plant parts sampled included seedlings, terminals with two expanded leaves, leaves from the upper, middle, and lower sections of the canopy, white flowers, and medium-sized bolls. Adult thrips were significantly more abundant on seedlings and flowers in 2014, and on flowers followed by seedlings and leaves from the middle canopy in 2015. Immature thrips were significantly more abundant on seedlings, followed by flowers in 2014, and on seedlings followed by leaves from the lower canopy and flowers in 2015. Across locations and plant parts, thrips consisted of Frankliniella tritici (Fitch) (46.8%), Frankliniella fusca Hinds (23.5%), Frankliniella occidentalis (Pergande) (17.1%), Neohydatothrips variabilis (Beach) (7.4%), Thrips tabaci (Lindeman) (1.8%), and other species (3.4%). Frankliniella fusca represented 86.7% of all thrips on seedlings, while F. tritici was more abundant on terminals (51.6%), squares (57.5%), and flowers (75.1%). Across all leaf positions, F. fusca was the most abundant species (28.8%), followed by F. tritici (19.2%), N. variabilis (18.8%), F. occidentalis (12.9%), and T. tabaci (5.2%), as well as other species (15.0%). As neonicotinoid insecticides remain a primary tool to manage seedling infestations of F. fusca, our data indicate that mid- to late-season applications of neonicotinoid insecticides targeting other insect pests will intensify selection pressure for resistance on F. fusca, the primary pest of seedling cotton.