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As the scale of Web services is becoming larger, there are always noise data in the system. In order to improve the robustness of fault diagnosis of the Web services, this paper studies the problem of fault diagnosis for Web services. Firstly, we proposed an automatic diagnosis framework for Web service. Secondly, we defined the transition and emission matrixes, respectively, and used these matrixes to represent the state transition of Web services. Finally, we proposed a Viterbi based fault diagnosis algorithm. The experiments show that, the proposed algorithm has higher accuracy than related works, and has good robustness for noise data in Web services.