Summary With the rapid development of smartphones in recent years, we have witnessed an exponential growth of the number of mobile apps. Considering the security and management issues, network operators need to have a clear visibility into the apps running in the network. To this end, this paper presents a novel approach to generating the fingerprints for mobile apps from network traffic. The fingerprints that characterize the unique behaviors of specific mobile apps can be used to identify mobile apps from the real network traffic. In order to handle the large volume of traffic efficiently, we use non‐negative matrix factorization (NMF) to perform traffic analysis to cluster similar network traffic into groups. Then, access patterns of individual apps that are extracted from each group can be used as fingerprints distinguishing apps from others uniquely. The experimental evaluations show that the proposed approach can identify the mobile apps from random and mixed network traffic with high precision. Copyright © 2015 John Wiley & Sons, Ltd.