An automatic fingerprint identification system (AFIS) includes two stages,i.e. registration and authentication. At the atregistration stage, most AFISs store multiple template fingerprints of the same finger per user. When authenticating, the input fingerprint is compared with these multiple templates. This paper proposes merging features of multiple template fingerprints.Only the merged template is stored in the template database. When authenticating, the number of templates with which the input fingerprint is compared is decreased, thus the authentication is sped up. At the same time, it helps to improve the recognition accuracy so that the merged template contains more features than a single template. Experiments show that our method can achieve improved system performance.