The operational modal analysis as one of the applied and executive branches of system identification plays a very important role in extracting and determining the dynamic characteristics of structures based on the results of ambient vibration tests. One of the well-known methods of operational modal analysis is frequency domain decomposition (FDD) that identifies the modal parameters of the structural systems based on output only, with emphasis on white noise input. In recent years, a new approach, called Transmissibility based Operational Modal Analysis (TOMA), has also been introduced in which there is no limit to the input excitations of the system. One of the most important methods of the effective approach is singular value decomposition of the power spectral density transmissibility matrix (PSDTM-SVD). In the present paper, seismic responses of a 5DOF system under the excitation of Loma Prieta earthquake with the different signal to noise ratios are used to investigate and compare the performance of FDD and PSDTM-SVD methods in the presence of white noise. Comparison of the results indicates that the PSDTM-SVD transmissibility method has a better performance than the FDD method in identifying the vibrational modes of the system, so that by increasing the noise level in the system responses, the more prominent modal peaks are obtained in the spectra. However, in the FDD method, no appreciable change is made in the first single value spectra by increasing the noise level in the signal.