In recent years, the new varieties breeding of common bean has been developing rapidly, and the number of new varieties and applications for Plant Variety Protection (PVP) has been increasing. In order to protect the legitimate rights and interests of breeders, regulate the seed market and improve the efficiency of the seed market supervision, this study intends to establish common bean identification system based on a set of SSR molecular markers. Firstly, 12 common bean varieties with different origins and botanical morphology were selected, and 120 SSR markers with high polymorphism and clear bands were screened by polyacrylamide gel electrophoresis. Then, 33 SSR core markers with even distribution, high polymorphism and stable peak pattern were obtained in 96 common bean varieties by fluorescence capillary electrophoresis. On this basis, the core markers were grouped according to the length of amplified fragments and the color of fluorescent markers, and reference varieties were set to correct the errors between different experimental batches and platforms. A variety identification system based on SSR markers was thus established. Meanwhile, a fingerprint database was constructed for 161 common beans for which plant variety protection was applied or which are protected varieties or dominant varieties or landraces. 140 varieties can be distinguished by the set of core markers, and the average genetic similarity coefficient is 0.33, showing a high genetic diversity of those varieties. 21 varieties that are not distinguished share high similarities in terms of origin, parentage and botanical characters, but they could still be recognized by some traits. The result indicates that the set of core markers are effective in aiding screening of similar varieties. The identification system of common bean based on SSR molecular markers established in this study will provide strong support for variety identification and for assisting selection of similar varieties in DUS tests.