Abstract:In order to understand the phylogenetic relationships in genus Lycoris, the atpB-rbcL spacer regions of chloroplast DNA (cpDNA) were sequenced from selected 95 taxa, including 15 species, 4 varieties and 2 hybrids. The results showed that 95 taxa were clearly classified into two main clades from phylogenetic tree based on atpB-rbcL sequences. There were close relationship among L. radiata var. pumila, L. sprengeri, L. caldwellii, L. albiflora, L. straminea and L. houdyshelii. The interspecific relationship revealed by atpB-rbcL sequences is partially consistent with morphological and karyotype classification. The species with subtelocentric chromosome grouped Clade I, and the species with telocentric and metacentric chromosomes formed Clade II. The species with subtelocentric, telocentric and metacentric chromosomes dispersed in the two clades, it verified the hypothesis that Lycoris species with subtelocentric, telocentric and metacentric chromosomes were hybrid origin. Combining the data from two artificial hybrids, atpB-rbcL sequence analysis also revealed that subtelocentric chromosomes of L. albiflora and L. caldwellii derived from L. sprengeri, while those of L. houdyshelii and L. straminea from L. radiata var. pumila.