Thrips cause damage to seedling cotton, and they are associated with the spread of Fusarium hardlock, a serious disease affecting cotton bolls that reduces lint yield in the southern United States. The population dynamics and within-plant distribution of Frankliniella spp. thrips in cotton were determined in 2005, 2006, and 2007 in Quincy and in 2006 and 2007 in Marianna, FL. Frankliniella tritici (Fitch) was >98% of the adult thrips collected. The adults of F. bispinosa (Morgan), F. occidentalis (Pergande), and F. fusca (Hinds) also were collected. Populations of F. fusca inhabited the cotton leaves of vegetative-stage cotton. The other species were highly anthophilic, primarily inhabiting cotton during its reproductive growth stages. Densities of these species peaked during mid-season, which also coincided with peak bloom. The adult F. tritici and the thrips larvae were aggregated in the flowers over the other plant parts, with more collected in the upper than the lower canopies. These patterns of aggregation were observed at each location each year, and the numerical differences usually were significant (P < 0.05). Densities of adult F. tritici were low on the leaves, squares, and bolls. The population dynamics and with-plant distribution of individual thrips species has not previously been determined for cotton in the southern United States.