Palazzo Marchesale in San Giuliano di Puglia (Italy) is an old masonry structure hosting the new City Hall. It is quite complex and is characterized by several parts with different height and foundation levels, and includes an internal court. After the earthquake of October 31st (ML =5.4) and November 1st, 2002, (ML =5.3), the building was retrofitted and seismic joints were realized between the different buildings, in order to regularize the dynamic behaviour. The structure has been considered for seismic monitoring in the framework of a research project funded by the Office for the reconstruction of San Giuliano di Puglia. Therefore a permanent accelerometric array has been designed and installed. It was tested by deploying also a temporary array in different configurations and recording ambient vibrations and weak motion effects. The experimental results were compared with those obtained by means of a finite element model. Thus, linear and nonlinear analysis allowed to evaluate the seismic safety of the structure. Modal identification and model updating are shown in the paper. © 2013 Taylor & Francis Group, London, UK.