Structural Health Monitoring (SHM) evaluates the integrity of a structure by observing its dynamic responses by an array of sensors over time to determine the current health state of the structure. The most important step of SHM is system identification which in civil structures is the identification of modal parameters of structures. Due to numerous limitations of input-output methods, system identification of ambient vibration structures using output-only identification techniques has become a key issue in structural health monitoring and assessment of engineering structures. In this paper, four beams with different boundary conditions and with arbitrary loading have been modeled in finite element software, ANSYS, and the responses (Acceleration of nodes) have been achieved. By using these data and the codes written in MATLAB software, the modal parameters (natural frequencies, mode shapes) of the beams are identified with FDD (frequency Domain Decomposition) and PP (Peak Picking) methods and then justified with the results of input-output method which was determined by frequency relation function (FRF). The results indicate a good agreement between the three methods for determining the dynamic characteristics of beams.