The detection of changes in the dynamic behavior of structures is an important issue in structural safety assessment. Deployment and servicing of marine and coastal structures such as piers in the marine environment constantly changing, requires understanding the dynamic behavior of these structures to prevent possible damage. Among the factors of uncertainty in understanding the dynamic performance of piers is uncertainties related to semi-rigid connection of deck to piles. According to this fact that the main mass of the structure is on deck, the connection of deck to piles is very important. In this study, experimental and numerical models of beach piers were studied. A test on experimental modal analysis was performed to determine the response of structures. A numerical model of the structure was prepared and theory of modal analysis was performed on it. Then, based on solution of optimization problem using Continuous Ant Colony Algorithm, the percentages of semi-rigid connections were determined and model was updated. Results show that the connection is not fully rigid. The present method can be used to determine the percentage of semi-rigidity of connections and prepare the finite element model to be more adaptable to the experimental model. Updated results with this method were very close to the real model.