Abstract: Lily flower colors are derived mainly from anthocyanins and carotenoids，and anthocyanins are the major pigment in pink and chocolate brown cultivars，whilst carotenoids in yellow and orange cultivars，and both anthocyanins and carotenoids contribute to red ones. The genetic mechanism and biosynthetic pathway of pigments are complicated in lily. It is documented that several genetic linkage maps of lily populations have been preliminarily constructed，and several quantitative trait locis related with flower color were also mapped. Many structural genes involved in the biosynthesis of anthocyanin and carotenoid have been isolated and identified. The transcription factor LhMYB12 involved in anthocyanin pathway regulates anthocyanin biosynthesis and determines the presence or absence of anthocyanin pigmentation in tepals，its transcript level affects the intensity and pattern of anthocyanin color. The better understanding on pigment biosynthetic pathway is helpful for breeding to change flower color by engineering the pathways in lily cultivars.

Key words: Lilium, flower color, breeding, transcription factor