This paper discusses on the output only modal identification of historic structures. Modal identification has been carried out both in frequency and in time domain using the Frequency Domain Decomposition (FDD) and the Stochastic Subspace Iteration (SSI-data) respectively. To highlight the sensitivity of the two methods, two masonry towers under different environmental loads have been considered. In one case the dynamic excitation can be assumed as a very weak random white noise, in the other case, probably due the several external noises, the ambient noise is locally dominated by several harmonic forces. The paper highlights the challenges in the modal identification of heritage structures such as the very low weak operating response and the role of the harmonics originated by engines operating somewhere nearby the structures. Moreover, it is investigated the information trade-off between the frequency domain and the time domain identification for evaluating the modal properties of the structures in a straightforward manner.