Abstract: Based on previous study of Orobanchaceae,we added sequence data of the genus Cistanche,used maximum parsimony,maximum likelihood and Bayesian inference to perform phylogenetic analysis,and investigated the systematic position of Cistanche in Orobanchaceae, as well as the generic relationships within Orobanchaceae. The phylogenetic trees respectively basing on sequences of rps16 and rps16+ITS revealed that Cistanche,Orobanche,and Boschniakia formed a one single clade,Cistanche was a sister to Orobanche,and holoparasi-tic,semiparasitic and non-parasitic taxon in Orobanchaceae fell into three separate clades.