A method and apparatus for allocating and signaling ACK/NACK resources in a wireless communication system are provided, in which a Node B determines to use ACK/NACK resources within a predetermined fixed-size first resource group for ACK/NACK transmission for non-persistently scheduled data channels, the ACK/NACK resources being implicitly mapped to SCCHs carrying scheduling information about the non-persistently scheduled data channels, and allocates ACK/NACK resources within a predetermined flexible-size second resource group for ACK/NACK transmission for persistently scheduled data channels and transmits resource indication information explicitly indicating the allocated ACK/NACK resources to at least one UE.