A method and system for allocating resources in a communication system are provided. The system includes a Base Station (BS) for allocating persistent resources included in a persistent resource area to one or more a Mobile Stations (MS) using the persistent resource area, for allocating an Identifier (ID) indicating an allocation order of the persistent resources to each of the one or more the MS using the persistent resource area, for transmitting resource allocation information including the ID and the number of slots included in the persistent resources to each of the one or more MSs using the persistent resource area, and for allocating dynamic resources to one or more MSs using a dynamic resource area, after the persistent resource allocation is completed for all of the one or more MSs using the persistent resource area. The persistent resource area includes successive persistent resources along a time axis and along a frequency axis.