A method for allocating frequency resources by a Base Station (BS) in a frequency overlay system is provided. The method includes grouping at least one Mobile Station (MS) capable of using the same Frequency Allocation (FA), according to zones, multicasting zone information indicating a frequency resource available for each zone to at least one MS belonging to a corresponding zone, unicasting resource allocation information indicating an allocated frequency resource to at least one MS to which the frequency resource is allocated, among the grouped MSs, and communicating with the at least one MS using the allocated frequency resource indicated by the resource allocation information, within the frequency resource indicated by the zone information.