Objective: To determine the genetic diversity of Cistanche species.
Method: Two populations of Cistanche deserticola and four populations of C. tubulosa were analyzed by random amplified polymorphic DNA (RAPD) markers.
Result: A total of 76 and 87 loci were amplified using 10 random primers each other. The average percentage of polymorphic loci of C. deserticola was 47.37%. The PPL were 39.47% and 35.53% for two populations. Average Nei's gene diversity was 0.1358, Shannon' s genetic diversity was 0.2072, and Gst was 0.2546. The average PPL of C. tubulosa was 27.59%. It was 19.54% to 25.29% in different populations and Andi'er population had the highest. Average Nei's gene diversity was 0.0823, and Shannon' s genetic diversity was 0.125 8, Cst was 0.175 5.
Conclusion: The diversity of Cistanche deserticola is higher than that of C. tubulosa, but both has differentiation among populations, C. deserticola has already separated itself into two different ecotypes.