© 2021, Istanbul Teknik Universitesi, Faculty of Architecture. All rights reserved.Istanbul is home to numerous architectural heritage which are in a great variety built by Byzantine and Ottoman period. On the other hand, cultural heritage buildings are faced with serious earthquake risks which require the investigation of the structural behaviour of cultural heritage buildings and the taking of necessary conservation measures to preserve and transfer them to the future in a sustainable way. This article describes an experimental in-situ investigation of an 18th century historic masonry monument, Nur-u Osmaniye Mosque in Istanbul by the non-destructive testing. Dynamic system identification study based on operational modal analysis (OMA) tests which include two different test setups in terms of locations and numbers of accelerometers. The extracted dynamic parameters of structure such as natural frequencies, mode shapes and as well as damping ratios obtained from two different test setups compared. In addition, the results of non-destructive in-situ tests used for the 3D Finite Element (FE) model updating by comparing and calibrating numerical and experimental characteristics. The paper presents an in situ dynamic identification procedure of an historic masonry monument based on operational modal analysis and compares dynamic properties obtained from experimental and numerical studies and gives the results of FE model updating of the structure.