This paper addresses the parameter identification of a one-link flexible manipulator based on the experimental measurement of the inputs/outputs, the finite element model, and the application of evolutionary algorithms. A novel approach is proposed to find the values of inertia, stiffness, and damping parameters by minimizing the difference between the numerical model’s outputs and the testbed’s outputs, thus considering the joint position and acceleration of the link’s tip. The dynamic model is initially obtained using the finite element method and the Lagrange principle. A prototype of a single one-link flexible manipulator is used in the experimental application, wherein the servomotor applies the input torque, and the outputs are the joint angle and the link’s tip acceleration. Then, an optimization problem minimizes the difference between the numerical and experimental outputs to determine the set of parameters using evolutionary algorithms. A comparative analysis to obtain the identified parameters is established using genetic algorithms, particle swarm optimization, and differential evolution. The proposed identification approach permitted the determination of the dynamic parameters based on the complete dynamic model of the flexible-link manipulator, which is different from the approaches reported in the literature that identify a simplified model. This information is essential for the design of the motion and vibration control laws.