Abstract: To confirm the anatomical structure and distribution of endophytes in the vegetative organs of different aged ginkgoes, we observed the anatomical structure of Ginkgo biloba L.roots, stems and leaves by paraffin section. Results showed that:(1) The root of annual G. biloba did not have a resin canal, but did have a few endophytes and a large number of albuminous cells in the cortex cells. The perennial root had a resin canal and many endophytes, as well as needle-like crystals, but did not have albuminous cells. (2) The young stem had an obvious cuticle, numerous albuminous cells in the cortex cells, and a developed phloem ray and central pith. The latter consisted of a large number of parenchyma cells, with albuminous cells and crystal druses but without a resin canal in the pith. (3) The spongy tissue of G. biloba leaves had a loose structure. There were resin canals and crystal druses in the mesophyll cells, and stomata with invagination under the epidermis, indicating that G. biloba had anatomical characteristics for drought tolerance. Based on the structure of the vegetative organs, this study helps clarify the relationship between different aged G. biloba and the ecological environment and provides reference for the further study of G. biloba endophytes.