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The multilevel fast multipole algorithm (MLFMA) based on the Nyström discretization of surface integral equations (SIEs) is developed for solving electromagnetic (EM) scattering by large composite objects. Traditionally, the MLFMA is based on the method of moments (MoM) discretization for the SIEs and it usually works well when the robust Rao-Wilton-Glisson (RWG) basis function is enough to represent unknown currents. However, the RWG basis function may not represent both the electric and magnetic current in solving the electric field integral equation (EFIE) and magnetic field integral equation (MFIE) for penetrable objects, and how one represents another current could be a problem in the MoM. In this work, we use the Nyström method as a tool to discretize the SIEs and incorporate the MLFMA to accelerate the solutions for electrically large problems. The advantages of the Nyström discretization include the simple mechanism of implementation, lower requirements on mesh quality, and no use of basis and testing functions. These benefits are particularly desired in the MLFMA because the solved problems are very large and complex in general. Numerical examples are presented to demonstrate the effectiveness of the proposed scheme.