A system and method for transmitting and receiving frequency allocation information based on identification information in a frequency overlay system are provided. The method includes transmitting a frame of a first Frequency Allocation (FA) to Mobile Stations (MSs) by inserting control information and identification information of the MSs to which frequency resources are allocated into the first FA frame, and transmitting a second frame indicating a second FA the MSs by inserting the identification information and a resource indication of the first FA into the second FA frame. Thereby, an overhead can be reduced and a frequency resource can be used efficiently.