The present invention provides a reference signal transmission method and apparatus by a base station in a wireless communication system including a relay station. The base station generates a plurality of relay-physical downlink control channel (R-PDCCH) reference signals for the demodulation of an R-PDCCH which is a control channel for the relay station relative to each of a plurality of layers, maps the plurality of R-PDCCH reference signals with R-PDCCH regions included in a relay zone within at least one resource block according to a predetermined reference signal pattern, and transmits at least one resource block through a plurality of antenna ports.