Objective To obtain the full-length gene and functional domains of FXYD6 gene which is a cholangiocarcinoma related gene. Methods A new strategy with the integration of bioinformatics and molecular biology was used. Bioinformatical methods were used to analyze the full-length sequence, and to predict the functional domains of its protein. And the full-length sequence of FXYD6 was isolated by polymerase chain reaction from fetal hepatic, brain and spleen cDNA libraries, and then cloned in pGEM-T vector for sequence analyzing. Goldkey Sequence Analyzing Software was used to analyze the sequence of candidate domain without signal peptide.Results The full-length sequence of FXYD6 was isolated by Touch-down PCR from fetal hepatic and brain cDNA library, but was not from spleen cDNA library. The open reading frame Finder software was used in the National Center for Biotechnology Information website to find the most probable encoding regions of FXYD6 gene. And the +1 phase was selected as the template sequence, from 67 bp to 354 bp, to predict the functional domains by Goldkey Sequence Analyzing Software. The signal peptide was located from 1 amino acid (aa) to 17 aa， and the main domain was composed from 18 aa to 34 aa. The region between 35 aa and 57 aa was the transmembrane region. The FHYD peptide chain was highly conserved amino acids. Conclusion The study of full-length cDNA cloning of FXYD6 gene and its functional domains provides the basis for understanding the relationship between the structure and function of FXYD6. More work shall be performed on FXYD6 protein and its influence on the mechanism of cholangiocarcinoma.