A method of transmitting a control signal in a wireless communication system is provided. The method includes acquiring a resource index, the number of cyclic shifts (CSs) and a CS interval, wherein the number of CSs is an integer multiple of the CS interval, determining a CS index based on the number of CSs and the CS interval, generating a cyclically shifted sequence by cyclically shifting a base sequence by a CS amount obtained from the CS index, generating a modulated sequence based on the cyclically shifted sequence and a symbol for a control signal and transmitting the modulated sequence after mapping the modulated sequence to a resource block obtained from the resource index.