A method for allocating resources in an Orthogonal Frequency Division Multiple Access (OFDMA) mobile communication system where data is transmitted by Hybrid Automatic Repeat reQuest (HARQ) is provided, in which a multiplexing mode is selected for multiplexing a Distributed Resource Channel (DRCH) and Localized Resource Channel (LRCH) over orthogonal frequency resources, in which it is determined whether to use persistent resource allocation for each slot, if the selected multiplexing mode is a multiplexing mode that punctures the DRCH onto the LRCH, resources are allocated in an Synchronous HARQ S-HARQ scheme if the persistent resource allocation is used, and resources are allocated in a Resource Adaptive S-HARQ (RAS-HARQ) scheme if the persistent resource allocation is not used and resources are to be reused when early termination of HARQ transmission occurs.