The genetic diversity of 16 Ganoderma strains was investigated by rDNA-ITS sequencing. Alignment analysis showed that whole length of internal transcribed spacer(ITS1+ITS2) was 500bp and with 139 variation sites (accounting for 23.3％, ITS1 was 66 and ITS2 was 73), 337 conserved sites (accounting for 72.2％), 59 informative sites (accounting for 9.88％), 86 conversion sites (G-A, C-T), 13 transversion site(C-G, T-A). The ratio of transition and transversion in ITS1 was higher than that in ITS2, and the variable sites of ITS2 were more than those of ITS1. The genetic distance among 16 Ganoderma strains is from 0 to 0.121. The genetic distance between G. lipsiense and F-1 was 0, and the genetic distance between Heizhi 02 and Huizhou, Jingda, G. capense was 0.121, 0.117 and 0.120, respectively. The 16 Ganoderma strains were classed into 4 groups. The biggest group is comprised of 12 strains, including Xinzhou, Huizhou, Jingda, 902, F-1, Xianzhi, Meiluo, Taishan, G. applanatum, 05, G. luteomarginatum. The G. atrum and G. sinense were clustered into one group. The G. capense and Zhongzhi was independent group, respectively. These results showed that there were some genetic difference among groups, and there was lower genetic diversity among strains in same groups.