In this study, the SRAP reaction system of Zelkova schneideriana was established. Combining capillary electrophoresis technology, fingerprinting and genetic cluster analysis were studied for seventy superior individuals of Zelkova schneideriana collected from Guizhou, Jiangxi, Zhejiang province and Kyoto of Japan. Totally 2276 bands were generated with 13 pairs of SRAP primers, of which all were polymorphic and each pair could separate all samples. Genetic distance among 70 superior individuals was 0.0078～0.3772 with an average value of 0.0629, while genetic similarity coefficient was 0.9218～0.9565 with an average value of 0.9339. This suggests that the genetic distance of zelkovas was close and the genetic similarity was high. The cluster analysis based on SRAP markers revealed that the classification of zelcovas related with their origin time, geographic location and the phenotypes such as autumn color and glossy degree of leaves. This study could be useful in identification, genetic resource management and protection of plant breeders` rights in Z. schneideriana.