Masonry heritage structures are among the most vulnerable typologies during earthquake. Their safety assessment requires a higher degree of accuracy due to the lack of knowledge on the original design and the construction procedures. The collection of information about the hidden geometry and the material properties should be performed by non-destructive techniques to avoid any damage to the artistic value. Moreover, for the assessment of the structural behavior of the tower a reliable method is the structural identification by on-site dynamic test. In this paper the results of the behavior ambient vibration test and operational modal analysis are reported to calibrate a FE model of the historical masonry bell-tower of S. Sofia. The bell tower of S. Sofia is part of the monumental complex of S. Sofia, in Benevento together with the S. Sofia church, the monastery and the fountain. In 2011, this monumental complex was added in the World Heritage List of UNESCO. The bell tower is about 27 meters high and it is characterized by a shaft which extends for a height of about 12 m, it has the shape of a hollow parallelepiped with a square base. The belfry is characterized by regular and equal openings on all four faces and it is surmounted by an octagonal lantern with a dome with eight segments. The calibrated model of the tower is used for the verification of the structure under vertical loads and seismic actions, because the location is an area of high-medium hazard.