The loquat germplasm of egg-shaped Ruantiao Baisha mutant, Ruantiao Baisha and five domestic cultivars were used to identify the variation of germplasm using morphological traits investigation and SRAP. 18primers which could produce clear and polymorphic bands were screened out from 96 ISSR random primers. 135 locis were detected ,of which 102were polymorphic and the polymorphic percentage was 75.6%.The genetic similarity coefficients of the loquat germplasms were among 0.53～0.89. 31 white flesh loquat germplasms were divided into four groups when the similar coefficient was 0.65. All the loquat germplasms come from Zhe Jiang province were clustered together in the first group.The second group contain 19 germplasms coming from China ,Japan and New zealand. .The genetic similarity coefficients between 0.58 and 0.89. The third group contain Shanghai Baisha and Guangxin Bami. The fourth group include Baili and Longcai Bai .As the key research object, GS between egg-shaped Ruantiao Baisha and reference were among 0.55~0.88. It had the maximum genetic simlity with Bai Lizhi, and minimun genetic simlity with Wu Gong Bai. GS of egg-shaped Ruantiao Baisha and Ruantiao Baisha was only 0.73. The study of biological characters, There were obvious differences among fruit shape,seed number and edible rate of egg-shaped Ruantiao Baisha and Ruantiao Baisha The results showed that the egg-shaped Ruantiao Baisha mutant and Ruantiao Baisha loquat has obvious difference in characters such as fruit shape, seed numbers and edible rate. The analysis confirmed the obvious genetic variation between the egg-shaped Ruantiao Baisha and Ruantiao Baisha loquat. This study is important to apply new varieties identity and protection of intellectual property rights for the egg-shaped Ruantiao Baisha mutant.