The thesis focused on the resource allocation problem in wireless networks in the presence of flow-level dynamics. The first problem investigated is the scheduling problem in the downlink transmission of wireless cellular networks, including single-channel and multi-channel networks. Throughput-optimal scheduling algorithms were developed in both networks. Then, the joint congestion control and scheduling problem in wireless peer-to-peer networks was investigated. An optimal architecture which can maximize the social welfare while satisfying the delay constraints of packets was proposed. At last, in Chapter 5, my work on the scheduling problem in multihop wireless networks was described. The scheduling algorithm developed in this chapter was proved to be throughput optimal and has superior performance than previous algorithms.