A reliable procedure to identify the dynamic behaviour of existing masonry buildings is described in the paper, referring to a representative case study: a historical masonry palace located in Benevento (Italy). Since the building has been equipped with a permanent dynamic monitoring system by the Department of Civil Protection, some of the recorded data, acquired in various operating conditions, have been analysed with basic instruments of the Operational Modal Analysis in order to identify the main eigenfrequencies and vibration modes of the structure. The obtained experimental results have been compared to the numerical outcomes provided by three detailed Finite Element (FE) models of the building. The influence of Soil-Structure Interaction (SSI) has been also introduced in the FE model by a sub-structure approach where concentrated springs were placed at the base of the building to simulate the effect of soil and foundation on the global dynamic behaviour of the structure. The obtained results evidence that subsoil cannot a priori be disregarded in identifying the dynamic response of the building.