Abstract: Gentiana lawrencei var. farreri, which has medical and gardening value, is a common species in Gentiana and distributes on the Qinghai-Tibetan Plateau. Nuclear ribosomal internal transcribed spacer (ITS) is a common molecular marker used in phylogenetics and population genetics， but has difficulty in sequencing and data analysis due to heterozygosity. A total of 39 individuals from 7 populations of G. lawrencei var. farreri were sequenced after cloning in this study. The obtained 81 sequences identify 76 haplotypes in total. For the genetic variations, 87.61% occured within population and only 12.39% occured among populations. Haplotypes, which were rarely shared among individuals （2.64%）, did not show a clear phylogenetic relationship. In conclusion, this study showed high ITS heterozygosity in G. lawrencei var. farreri and would be helpful in researches about Gentiana evolution.

Key words: Gentiana lawrencei var. farreri, ITS, heterozygosity, genetic divergence