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An alternate parallel receiver (APRX) has been developed jointly by the Jet Propulsion Laboratory and Goddard Space Flight Center. Time-domain equalization used to suppress multipath interference is very sensitive to the echo length, which will be very large when the symbol rate goes high. To solve this problem in high data-rate transmission, this paper proposes a feedback frequency-domain equalization (FFDE) method for the APRX. Based on the specific frame structure using PN sequence as frame head, channel impulse response can be estimated by correlating the received PN head with the local PN sequence. The coefficients of the frequency-domain equalizer used in the next frame can be updated by compensating the current equalizer coefficients with the estimated channel frequency response in the current frame. Simulations verify the efficiency of the proposed FFDE scheme in frequency selective channels.