Modal identification based on ambient vibration data has attracted extensive attention in the past few decades. Since the excitation for ambient vibration tests is mainly from the environmental effects such as wind and traffic loading and no artificial excitation is applied, the signal to noise (s/n) ratio of the data acquired plays an important role in mode identifiability. Under ambient vibration conditions, certain modes may not be identifiable due to a low s/n ratio. This paper presents a study on the mode identifiability of an instrumented cable-stayed bridge with the use of acceleration response data measured by a long-term structural health monitoring system. A recently developed fast Bayesian FFT method is utilized to perform output-only modal identification. In addition to identifying the most probable values (MPVs) of modal parameters, the associated posterior uncertainties can be obtained by this method. Likewise, the power spectral density of modal force can be identified, and thus it is possible to obtain the modal s/n ratio. This provides an efficient way to investigate the mode identifiability. Three groups of data are utilized in this study: the first one is 10 data sets including six collected under normal wind conditions and four collected during typhoons; the second one is three data sets with wind speeds of about 7.5 m/s; and the third one is some blind data. The first two groups of data are used to perform ambient modal identification and help to estimate a critical value of the s/n ratio above which the deficient mode is identifiable, while the third group of data is used to perform verification. A couple of fundamental modes are identified, including the ones in the vertical and transverse directions respectively and coupled in both directions. The uncertainty and s/n ratio of the deficient mode are investigated and discussed. A critical value of the modal s/n ratio is suggested to evaluate the mode identifiability of the deficient mode. The work presented in this paper could provide a base for the vibration-based condition assessment in future.