Abstract: Naturally allopolyploid cotton has been widely used as a suitable model to investigate gene expression remodeling as a consequence of polyploidization. In this study, through RNA-seq, we comprehensively investigated the expression patterns of homoeologous genes between allopolyploid cotton (G. hirsutum) and its diploid progenitors (G. arboreum and G. raimondii) at the fiber initiation development stage. In tetraploid cotton, genes showed expression level dominance bias toward the A genome, especially at 3 and 5 days postanthesis. This expression level dominance (ELD) bias toward the A genome was synergistically expressed by the up-/downregulation of the homeologs from the nondominant progenitor (D genome). Gene Ontology enrichment results indicated that the alteration in the gene upregulation patterns of ELD-A could be a prominent cause of the phenotypic variation in fatty acid biosynthesis and metabolism and microtubule procession, and the downregulation of ELD-A genes could be related to gene regulation from transcription and stress inducement. In addition, the number and proportion of completely A- and D- subfunctionalized genes were similar at different fiber development stages. However, for neofunctionalization, the number and proportion of reactivated D-derived genes was greater than that of A at 3 and 5 DPA. Eventually, the expression bias of homologous genes led to novel asymmetric transcripts between the two subgenomes at each stage after polyploidization and domestication, despite the highly conserved overall patterns of gene expression. Our study provides new insights into duplicate gene (homeolog) expression alterations at different fiber development stages of cotton after allopolyploidization.