In order to distinguish the main Ginkgo cultivars and genetic diversity among them, 44 main Ginkgo eultivars planted in Pizhou Ginkgo Germplasm Garden, Jiangsu, China were sampled and analyzed by molecular marker RAPD and ISSR. These cultivars are planted widely in China. The ISSR results showed that 44 main Ginkgo eultivars could be identified by 16 polymorphie sites amplified by 5 ISSR primers. A computerized ISSR fingerprinting of the 44 Ginkgo cultivars was drawn to facilitate the management of eultivars. The genetic diversity of the cultivar population was studied by RAPD and ISSR. The results showed that the average effective number of alleles, gene diversity and Shannon’s information index revealed were 1. 730 7,0. 410 1 and 0. 596 3 respectively by ISSR, and were 1. 573 5,0. 333 1 and 0. 497 9 respectively by RAPD, which indicated high genetic diversity among the population. ISSR marker was more accurate in assessing the genetic diversity of Ginkgo than that of RAPD. So it indicated that ISSR is a good molecular marker to distinguish Gingko cultivars, and it can be put into practical use when more cultivars are added and more appropriate primers are sequenced. As there exist high genetic diversity in Ginkgo cultivars, it is important to collect as many representative trees planted in different places as possible, in order to protect and exploit them better.