Rubber tree is an important tropical economic crop. Rubber clones are mainly identified by morphological characters, which is difficult due to the minor morphological differences among them. In order to establish a stable, accurate, and efficient method for rubber clone identification, 5 (out of 426) pairs of SSR primers with clear and stable amplification profiles were selected as core primer sets. Based on these primer sets, high throughput genotyping of 129 rubber tree clones were performed. A total of 71 bands were detected, all of which were polymorphic. The average PIC of the primer pairs was 0.69. According to the polymorphic bands, specific DNA fingerprint of each clone was successfully constructed, and all of the specific DNA fingerprints were converted into quick response (QR) code. The results indicated that an effective method for rubber tree clone identification was constructed, which can provide sufficient technological supports for the protection of rubber tree clone intellectual property.