Machine condition monitoring and diagnosis have become increasingly important, and the application of these processes to stationary structures and rotating machinery has been widely investigated. The authors previously proposed a stepwise diagnosis method. In that method, the location of the abnormality is first estimated using the force identification approach, and then the cause and the severity of the abnormality are identified. But the method was applicable for an abnormality of linear property. In this study, a stepwise diagnostic approach for a beam with an abnormality of nonlinear property, that is, a breathing crack, is proposed. In this method, the location and the severity of abnormality are identified by using the multi-frequencies of response under the abnormal condition. Using the numerical example of a uniform beam fixed at both ends, we confirmed the validity of the method and determined that the selection of the excitation frequency was very important. Moreover, we showed the applicability of the method by using experimental data. We conclude that the proposed diagnosis method is feasible for identifying the abnormality of a breathing crack.