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This paper explores the possibility of using a combination of the empirical modedecomposition (EMD) and the Hilbert transform (HT), termed the Hilbert-Huang transform (HT)method, to identify the modal damping ratios of the structure with closely spaced modal frequencies. Theprinciple of the HT method and the procedure of using the HT method for modal damping ratioidentification are briefly introduced first. The dynamic response of a two-degrees-of-fredom (2DOF)system under an impact load is then computed for a wide range of dynamic properties from well-separated modal frequencies to very closely spaced modal frequencies. The natural frequencies and modaldamping ratios identified by the HHT method are compared with the theoretical values and thoseidentified using the fast Fourier transform (FT) method. The results show that the HHT method issuperior to the FFT method in the identification of modal damping ratios of the structure with closelyspaced modes of vibration. Finally, a 36-storey shear building with a 4-storey light appendage, havingclosely spaced modal frequencies and subjected to an ambient ground motion, is analyzed. The modaldamping ratios identified by the HHT method in conjunction with the random decrement technique (RDT)are much better than those obtained by the FT method. The HT method performing in the frequency-time domain seems to be a promising tool for system identification of civil engineering structures.