A methodology for the formulation of dynamic equations of motion of a serial flexible-link manipulator using the decoupled natural orthogonal complement (DeNOC) matrices, introduced elsewhere for rigid bodies, is presented in this paper. First, the Euler Lagrange (EL) equations of motion of the system are written. Then using the equivalence of EL and Newton–Euler (NE) equations, and the DeNOC matrices associated with the velocity constraints of the connecting bodies, the analytical and recursive expressions for the matrices and vectors appearing in the independent dynamic equations of motion are obtained. The analytical expressions allow one to obtain a recursive forward dynamics algorithm not only for rigid body manipulators, as reported earlier, but also for the flexible body manipulators. The proposed simulation algorithm for the flexible link robots is shown to be computationally more efficient and numerically more stable than other algorithms present in the literature. Simulations, using the proposed algorithm, for a two link arm with each link flexible and a Space Shuttle Remote Manipulator System (SSRMS) are presented. Numerical stability aspects of the algorithms are investigated using various criteria, namely, the zero eigenvalue phenomenon, energy drift method, etc. Numerical example of a SSRMS is taken up to show the efficiency and stability of the proposed algorithm. Physical interpretations of many terms associated with dynamic equations of flexible links, namely, the mass matrix of a composite flexible body, inertia wrench of a flexible link, etc. are also presented.