Target region amplification polymorphism (TRAP) marker was occupied to study on the genetic diversity of fifty Liriope Muscari clones.Total eight genes, one lectin gene and seven related to fructose, photosynthesis and steroid saponin metabolism, were selected as target genes and used to design thirteen the anchored primers for pairing with nineteen arbitrary primers. And eleven combinations of primers were screened to be able to produce clear banding patterns and polymorphisms.The results showed that 335 bands were amplified totally by 11 pair TRAP primers, of which 323 bands (96.41%) were polymorphic in the species level The average of polymorphism information content (PIC) was 0.930. gene differentiation index (Gst) was 0.610. The results of cluster analysis based on UPGMA revealed genetic coefficient ranged from 0.52 to 0.98.A relatively high genetic diversity existed in L. muscari, a certain level of genetic differentiation among populations.