Structural health monitoring is essential for ensuring the structural safety performance during the service life. The process is of paramount importance in the case of the Pelamis wave energy converter due to the structural parts being subjected to the marine environmental risky conditions and consequently, power take-off system damage. In this paper, a fuzzy-based damage detection method using the dynamic response of the Pelamis type P1 is proposed. Accurate modeling of a dynamic system with simple dynamic equations is one of the important steps of damage detection process; for this purpose, the equations of the motion of the Pelamis system is derived using the Lagrangian method for creating a discrete model of the Pelamis in the first step. For validating the obtained model, scaled experimental model of the Pelamis is provided, and modal analysis is carried out. Then, the features in the frequency spectrum of the structure response in each degree of freedom as a result of power take-off damaged conditions are considered as inputs to the fuzzy system. Also, the fuzzy system is trained based on calibrating the membership functions by defining the damage classes appropriately. For validating the proposed method, noise with different signal to noise ratios is inserted to the measured features and the success rate of the damage detection is calculated. The results show that the proposed method is able to identify the damage classes with acceptable success rate.