Abstract: For further interpretation the apocarotenoid biosynthetic pathway in saffron, CsBCH1-z —a novel β carotene hydroxylase gene was isolated from stigma, and was cloned, which the full length of encoding region was 906 bps, contained 301 amino acid residues, and the corresponding to the genomic sequence of 1261bp, five exons separated by 4 introns. Compared with the amino acid sequence of the known CsBCH1 gene, there were two amino acids deletion and one amino acid changed from isoleucine to leucine caused by 6 bases deletion in the N- terminal, and another amino acid changed from threonine to alanine which was resulted in one SNP. It predicted CsBCH1-z protein contained 3 distinct transmembrane domains, C terminal contained two ‘HXXHH’ domain, was a typical fatty acid hydroxylase. As the key precursor of crocin synthesis, the expression level of CsBCH1-z was higher in stigma > leaves > petal, was very low in stamen, while was invisible in corm. The gene cloning and bioinformatics analysis of the novel saffron beta carotene hydroxylase provided the theoretical basis of the saffron active components biosynthetic process and accumulation.