In order to accelerate the identification process, a Frequency-Domain recursive hybrid Genetic Algorithm is developed. The time history of the measurement is divided into a series of time intervals, and then the model of equivalent linear system is employed to identify the modal parameters of the system for each time interval. The differential equation can be transformed into the frequency domain by finite Fourier transform and the response in the frequency domain can be solved by algebraic equations instead of differentials equations for each time interval. The process of exploring this new algorithm is similar to that of recursive hybrid genetic algorithm in the time-domain, by using the simulated MDOF system considering the effect of noise contamination. Finally, this new identification strategy is also applied to the identification of the real buildings. By employing the Maximum Softening Index, Approximate Story Damage Index and Modal Assurance Criterion, we can determine the damage states of these buildings. According to the damaged states of the buildings, a set of the reference values for damage states can be proposed and be applied to the damage assessment of a real building for future application.