Abstract: The cpDNA trnS-trnG intergenic spacer sequence of 14Ginkgo biloba var. epiphylla trees and 2 Ginkgo biloba trees were amplified and analyzed successfully.The results indicated that the size of trnS-trnG sequences was 1005bp and the content of A+T was 62.19%—62.39%.There were 23 variable sizes and one information size in this 14 Ginkgo biloba var. epiphylla trees and 2 Ginkgo biloba trees.There were little difference among the trnS-trnG sequences.YZ1 had more variable sizes and lower different areas with other samples.All the sequences through Blast found that it had a highly similar with Ginkgo biloba and cycas another.DNASTAR software was used to analysis indentity and diver gence and construct phylogenetic tree based on all the trnS-trnG sequences of 14Ginkgo biloba var. epiphylla trees and 2 Ginkgo biloba trees.