A mRNA preferentially expressed in cotton fiber was cloned from fiber total RNA of normal upland cotton TM-1 (wild-type) by using RT-PCR and corresponding cDNA (signed as TM-E6) was sequenced. TM-E6 gene had no intron and contained an open reading frame 771 bp long, and might encode a peptide of 246 amino acids. Other four genes, Fl-E6, Li-E6, N-E6 and Bl-E6, which were homologous to TM-E6 gene, also were isolated from four fiber mutants of Fiberless Xu-Zhou 142, Ligon lintless, Naked seed and Brown lint, respectively. Sequence analysis of each of these mutant genes revealed many variations in structure and nucleotide composition of gene when compared with sequence of TM-E6 gene. (1). There was a changeable repetitive segment in which GGCTCA (Gly-Ser) was repeated from three to five times between the 82nd and the 93rd codon in different mutant genes. Since the change of Gly-Ser repetitive segment occurred not only in the mutants but also in the wild-type cotton, the repeat frequency might be not associated with the mutation of fiber characteristics. (2). Among these four mutant genes, the percentage of changed codons was 7.05% in Fl-E6, 4.98% in Li-E6, and 4.15% in N-E6 and Bl-E6. It seems that the percentage of changed codons in E6 sequence was positively correlated to the degree of fiber morphological variation. (3). E6 polypeptides of Two long-fiberless mutants (Fiberless Xu-Zhou 142 and ligon lintless) contained high similar (99.4%) variation in the region of ~174 amino acids from N-terminus, and those of shor-fiberlees mutants (Fiberless Xu-Zhou and naked seed) revealed identical variation in the region from 116th to 220th amino acid. It also seems that there was a parallel relation between E6 protein variation and fiber phenotype mutation. (4). Li-E6 and Bl-E6 gene also expressed at low level in seed coat besides at high level in fiber.