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We propose a new method for direction of arrival (DOA) estimation in the presence of multipath propagation and mutual coupling for a frequency hopping (FH) system. With the use of pilot symbols and assuming perfect time-frequency synchronization for a linear array, we take mutual coupling and multipath propagation into account, and derive a maximum likelihood (ML) estimator for both the mutual coupling matrix and DOA estimation. We then formulate an iterative alternating minimization (AM) algorithm for finding the mutual coupling and DOA parameters in an alternate manner. Simulation results illustrating the performance of the algorithm and comparison with the Cramer-Rao bound (CRB) are also presented.