Application-level protocol specifications are helpful for network security management, including intrusion detection and intrusion prevention which rely on monitoring technologies such as deep packet inspection. Moreover, detailed knowledge of protocol specifications is also an effective way of detecting malicious code. However, current methods for obtaining unknown and proprietary protocol message formats (i.e., no publicly available protocol specification), especially binary protocols, highly rely on manual operations, such as reverse engineering which is time-consuming and laborious. In this paper, we propose Biprominer, a tool that can automatically extract binary protocol message formats of an application from its real-world network trace. In addition, we present a transition probability model for a better description of the protocol. The chief feature of Biprominer is that it does not need to have any priori knowledge of protocol formats, because Biprominer is based on the statistical nature of the protocol format. We evaluate the efficacy of Biprominer over three binary protocols, with an average precision more than 99% and a recall better than 96.7%.