A relaying method and system in a communication system having a Base Station (BS), a Mobile Station (MS) for communicating with the BS, and a Relay Station (RS) for relaying signals between the BS and the MS are provided. In the relaying method and system, the BS generates a BS pilot sequence and transmits the generated BS pilot sequence to the RS. wherein a partial cross correlation between the BS pilot sequence and an RS pilot sequence, being the BS pilot sequence relayed by the RS is always ‘0’. Accordingly, system capacity is more efficiently utilized.