With increasing demand for high-quality cotton, it is desirable to identify genes involved in fiber development for molecular improvement of cotton. In this study, 780 differentially expressed genes (DEGs) were identified in developing fibers at 10 days post-anthesis (DPA) in Gossypium hirsutum acc. DH962 and G. hirsutum cv. Jimian 5 using RNA-seq. Of 15 stable QTL for fiber quality identified in the same two parents in previous studies, 4, 3, 6, 1, and 1 QTL were associated with fiber length (FL), fiber strength (FS), micronaire (MIC), fiber elongation (FE) and fiber length uniformity ratio (FU), respectively. Integration of DEGs and QTL allowed the identification of 31 genes in 9 QTL regions, of which 25 were highly expressed in fibers based on the transcriptome datasets and 9 were preferentially expressed in different stages of fiber development. Gh_A01G0453 (GhDTX19), Gh_D07G1581 and Gh_D04G0942 were expressed specifically in 5 and 10 DPA fibers, with Gh_D04G0942 showing low expression in other tissues except pistil. Gh_D07G1799 (GhGAUT9), Gh_D11G0326 (GhVPS29), Gh_D11G0333 (GhTCP14), and Gh_D11G0334 (GhNRP2) were prefer-entially expressed in 5 or 10 DPA fibers;Gh_A01G0397 (GhABCG10) and Gh_D07G1744 were expressed specifically in 20 and 25 DPA fibers. These results suggest candidate genes for molecular improvement of cotton fiber quality.