In this study F3’H, F3’5’H and HCT genes from colored cotton were cloned and the HCT gene expression characteristics was analysized. Meanwhile we cloned three DFR genes color varieties with different colors and analysised these genes by bioinformatics. This research provides the theoretical basis and candidate genes for colored cotton color and quality improvement. The results are as follows: 1) With DPA16 of XC-5 leaves as material the F3’H and F3’5’H gene primers were designed according to the known CDS sequences in NCBI database and the genes were cloned by reverse transcription PCR technology. Meanwhile with DPA16 of XC -5 fibres as material the HCT primer was designed according to the sequence information of the Cotton genome databases and the genes were cloned by reverse transcription PCR technology.In the end we acquired the complete CDS sequences. They have high homology with known the gene sequences from other species. Homologous alignment indicated that the nucleotide similarity of Hibiscus cannabinus, Populus trichocarpa, Arabidopsis thaliana, Ricinus communis and Fragaria vesca is 81.76%, 73.90%, 72.58%, 71.74% and 73.11% with the HCT amino acid residues of XC-6. This research provides the basis for the further use of these gene resources in germplasminnovation of new colored cotton. 2) In this study, through homologous cloning technology, three complete CDSs encoding dihydroflavonol 4-reductase (DFR), which is a key enzyme in the pathway of anthocyanin biosynthesis and were cloned from the petal of petunia hybrid planted in Xinjiang with white, red and blue petal color respectively. The three DFR genes were named PhDFR1, PhDFR2 and PhDFR3. Homologous alignment indicated that the nucleotide similarity of three DFR is 97.79 %,96.59% and 97.99% with another DFR gene from Petunia hybrida ( GeneBank access number: X15537). All DFR cDNAs encoded a poly peptide composed of 380 amino acid residues. The mino acid residues similarity of three DFR is 95.53 %,94.21% and 95.79% with another DFR gene from Petunia hybrida ( GeneBank access number: CAA33544). DFRs of three colored Petunia hybrida varieties contain a highly conserved NADP(H)-binding site and substrate specificity site which belong to NADB-Rossmann superfamily. They were satable proteins without signal peptide and were hydrophilic proteins probably located in cytoplasm. All of them had transmembrane domains. α-helix and random coil were primary secondary structural components of DFR. Forming Rossmann folding of β-α-β-α-β and were symmetrical distributed on the whole.The phylogenetic analysis of DFR proteins from different species revealed that the PhDFR1、PhDFR2 and PhDFR3 had closer relationship with the known Petunia hybrida DFR . The cloning of these three DFR genes provided candidate genes for colored cotton genetic improvement. 3) Real-time fluorescent quantitative PCR experiments were conducted using XC-6 as material. The result: HCT gene was expressed in different tissues but in the minimum amount of relative expression in the leaf. The mRNA copy number of HCT gene is less than that of internal reference gene UBI.