Structural system identification (SSI) is an inverse problem of difficult solution. Currently, difficulties lie in the development of algorithms which can cater to large size problems. In this paper, a parameter estimation technique based on evolutionary strategy is presented to overcome some of the difficulties encountered in using the traditional system identification methods in terms of convergence. In this paper, a non-traditional form of system identification technique employing evolutionary algorithms is proposed. In order to improve the convergence characteristics, it is proposed to employ immune algorithms which are proved to be built with superior diversification mechanism than the conventional evolutionary algorithms and are being used for several practical complex optimisation problems. In order to reduce the number of design variables, domain decomposition methods are used, where the identification process of the entire structure is carried out in multiple stages rather than in single step. The domain decomposition based methods also help in limiting the number of sensors to be employed during dynamic testing of the structure to be identified, as the process of system identification is carried out in multiple stages. A fifteen storey framed structure, truss bridge and 40 m tall microwave tower are considered as a numerical examples to demonstrate the effectiveness of the domain decomposition based structural system identification technique using immune algorithm.