Dynamic identification is considered a powerful technique for testing the conservation status of buildings as their natural frequencies, damping and modal shapes are directly related to their rigidity and structural integrity. This issue is of crucial interest when historical structures are in area of high seismic level, as SanSepolcro city which has experienced earthquakes up to a maximum intensity of I max = X MCS scale. The dynamic response is suitable for ancient structures because is performed by measuring ambient vibrations instead of actively shaking the building. The results obtained from dynamic tests might be used to validate the assumptions used in numerical modeling in order to reduce the uncertainties related to the soil-structure interaction and to the structural parameters. In this framework, we show how an automatic identification procedure can track in real-time the dynamic response of the museum in Sansepolcro (Italy) using operational modal analysis (OMA). The dynamic characteristics, of the SanSepolcro museum and the wall supporting the mural painting of Resurrection of Christ, were identified by installing a temporary network of 10 seismic sensors. The OMA technique was performed using enhanced frequency domain decomposition (EFDD) which has allowed to detect the first four modal shapes, damping and structural frequencies. The dynamic characteristics were used to calibrate a more realistic and reliable 3D-FEM numerical model. Integrating, the results of the dynamic indetification with 3D-FEM model analysis, has provided important information to understand the complicated system of connections between the existing walls.