The phylogenetic relationship of Cistanche deserticola, C. salsa and C. tubulosa was analyzed by comparing the nucleotide sequences of the plastid rps2 gene and the intergenic spacer region between rpl16 and rpl14. By comparison of sequence data, the Cistanche samples were distinguishable from each other. The results were consistent with their anatomical and chemical characteristics. Intraspecific variations were found in C. salsa and C. tubulosa among the geographical populations. The NJ tree reconstructed based on the sequence data revealed that C. deserticola and C. salsa from China were closely related to each other, and C. tubulosa was placed as an outgroup of them.