New advances in molecular breeding of lily were reviewed in this paper. The first part is the gene cloning including meiosis genes, flower development genes, floral color genes, pollen development genes, and genes related to resistance. The second part is the establishment of regeneration system including adventitious shoot regeneration system, protoplast regeneration system, somatic embryo regeneration system, and callus regeneration system. The third part is gene transformation methods including Agrobacterium mediated genetic transformation, DNA directly into the system, gene transformation via pollen-tube pathway. The fourth part is the trangene application in lily. Meanwhile, the existing problems and prospects of the application of molecular breeding in lily were discussed.