Technical Abstract: Members of the auxin/indole-3-acetic acid (Aux/IAA) gene family encode proteins to mediate the responses of auxin gene expression and to regulate various aspects of plant morphological development. In this paper, we report the identification of nine cDNAs that contain complete open reading frame (ORF) and belong to Aux/IAA family in cotton (Gossypium hirsutum L.). They were designated GhAux1~GhAux9 (Gossypium hirsutum Aux/IAA), respectively. The amino acids encoded by these 9 genes either had whole or part of conservative domains of Aux/IAA superfamily with sequence identity ranging from 14 to 67%. None of them had typical signal peptide except GhAux8, and phosphorylation was one of the major ways involving the GhAuxs protein post-translational modifications. Semi-quantitative reverse transcriptase—PCR (RT-PCR) revealed that auxin could differentially induce expression of these GhAuxs genes, indicating their role in auxin signal transduction. Real-time quantitative RT-PCR analysis showed that the transcripts of GhAux1, GhAux2 and GhAux3 were abundant in vegetative organs, while GhAux4, GhAux5, GhAux6 and GhAux7 were preferentially expressed in ovules at the day of anthesis. GhAux8 was preferentially up-regulated in the stages of fiber elongation and secondary cell wall thickening. GhAux9 is specifically expressed in developing fibers with the expression peak at 10 days-post anthesis (10DPA) and no detectable expression in roots, stems, or leaves. Expression analysis of GhAux4, GhAux5 and GhAux7 in wild type TM-1, different lintless-fuzzless and linted-fuzzless mutants has further showed that these 3 genes were significantly up-regulated during the fiber initiation stage in fiber developmental mutants as compared with linted-fuzzed TM-1.