Abstract: Comparative morphology of the epiphyllous microsporangia in Ginkgo biloba L. firstly discovered in China were studied. There are normal microsporangia and epiphyllous microsporangia on the epiphyllous microsporangia Ginkgo, which accounted for 98% and 2%, respectively. The percentage of epiphyllous microsporangia leaf on the short shoot with epiphyllous microsporangia is 19.9%. The epiphyllous microsporangia often arise on the edges of leaves of short shoots. The leaves with epiphyllous microsporangia are obviously smaller than normal leaves in size. Usually 1 to 9 microsporangia cluster on the leaf lobes or about 1 to 3 (sometimes 5) microsporangia are born at the both sides of the petiole. The average length and width of the epiphyllous microsporangia are 4.95mm and 0.48mm respectively. Each microsporangia contains 18600 pollen grains. The length and width of the pollen grain is 27.57μm and 13.60μm, respectively. There are 64300 pollen grains in each epiphyllous microstrobilus. Their pollen grain has the ability of germination. Q-type clusters of long shoot and short shoot and microstrobilus and microsporangia show that three years old shoot and four years old shoot belong to one group. The essence of morphology, taxonomic status and genetic relationship of epiphyllous microsporangia Ginkgo were discussed. The finding of epiphyllous microsporangia Ginkgo was very important both to the protection and utilization of Ginkgo germplasm resources in China as well as the research on the essence of morphology of male reproductive organ in Ginkgo, taxonomic status and genetic relationship of Ginkgo.