As the foundation of further signal decoding, protocol identification technique plays a very important role in the information countermeasures. Furthermore, it is a key step for information countermeasures to evolve from signal layer to signal layer combined with information layer. The basic approach of unknown protocols identificated from massive bit-stream data is the bit stream data mining, and looking for information which can determine the type of protocol. In the case of lacking of prior knowledge, frequent pattern sequence appearing in the bit stream data needs to be extracted, and sequence that can identify the type of protocol should be screened out. In order to adapt to the environment of the bit stream, this paper makes an improvement based on the BNDM algorithm, and improves the efficiency of searching the frequent sequences in the binary environment. The experimental results show that unknown protocol identification, protocol data frame alignment and segmentation from massive bit-stream data are realized through the research results of this thesis.