An apparatus and method allocate resources in a communication system including at least one relay station (RS). A control channel carrying control information from a BS to an MS is allocated into a first time region of a subframe. A data channel carrying data from the BS to the MS, an RS-control channel carrying control information from the BS to an RS, and an RS-data channel carrying data from the BS to the RS are allocated into a second time region of the subframe, using Frequency Division Multiplexing (FDM). And the subframe into which the control channel, the data channel, the RS-control channel and the RS-data channel are allocated is transmitted.