The dynamic identification of the modal parameters of a structure, in order to gain control of its functionality under operating conditions, is currently under discussion from a scientific and technical point of views. The experimental observations obtained through structural health monitoring (SHM) are a useful calibration reference of numerical models (NMs). In this paper, the procedures for the identification of modal parameters in historical bell towers using a stochastic subspace identification (SSI) algorithm are presented. Then, NMs are manually calibrated on the identification’s results. Finally, the applicability of a genetic algorithm for the automatic calibration of the elastic parameters is considered with the aim of searching for the properties of the autochthonous material, in order to reduce modelling error following the model assurance criterion (MAC). In this regard, several material values on the same model are examined to see how to approach the evolution and the distribution of these features, comparing the characterization proposed by the genetic algorithm with the results considered by the manual iterative procedure.