A method of assigning a hybrid automatic repeat request (HARQ) process using a frequency division duplex (FDD) frame structure by a base station (BS) in a wireless communication system. The method according to one embodiment includes transmitting information related to a number of HARQ processes between the BS and a relay node (RN) to the RN. The number of the HARQ processes depends on subframes configured for transmission between the BS and the RN. The method according to the embodiment further includes assigning the HARQ processes subframes other than subframe indexes 0, 4, 5, and 9 based on the number of HARQ processes.