Abstract:In order to reveal the relationship of Dioscorea species, the interspecific molecular identification of 4 Dioscorea species, including D. sinopatviflora, D. zingibiernsis, D. bulbifera, and D. polystachya, were studied based on 4 cpDNA fragments, such as matK, rbcL, trnL-F and psbA-trnH, and these fragments on phylogenetic significance of Dioscorea genus was discussed. The results showed that the length of matK, rbcL, trnL-F and psbA-trnH fragments were 1026 - 1142 bp, 1156 - 1178 bp, 744 - 822 bp, 355 - 599 bp, respectively. According to the phylogenetic tree constructed by Bayesian Inference and PAUP 4.0b10 software, it was indicated that the genetic relationship of D. bulbifera in Yunnan was close to D. zingibiernsis, D. sinopatviflorawas close to D. zingibiernsis, while that of D. bulbifera in Africa was far to D. bulbifera in Yunnan. In addition, it couldn't be completely distinguished D. sinopatvifloraand D. zingibiernsis in the phylogenic tree by 4 combined fragments. So, it was suggested that the phylogeny evidence based on four fragments was not consistent with taxonomic classification of four species in Dioscorea.