Abstract: Wireless networks are developed under the fashion of wider spectrum utilization (e.g., cognitive radio) and multi-hop communication (e.g., wireless mesh networks). In these paradigms, how to effectively allocate the spectrum to different transmission links with minimized mutual interference becomes the key concern. In this paper, we study the throughput optimization via spectrum allocation in cognitive radio networks (CRNs). The previous studies incorporate either the conflict graph or SINR model to characterize the interference relationship. However, the former model neglects the accumulative interference effect and leads to unwanted interference and sub-optimal results, while the work based on the latter model neglects its heavy reliance on the accuracy of estimated RSS (receiving signal strength) among all potential links. Both are inadequate to characterize the complex relationship between interference and throughput. To this end, by considering the feature of CRs, like spectrum diversity and non-continuous OFDM, we propose a measurement-assisted SINR-based cross-layer throughput optimization solution. Our work concerns features in different layers: in the physical layer, we present an efficient RSS estimation algorithm to improve the accuracy of the SINR model; in the upper layer, a flow level SINR-based throughput optimization problem for WMNs is modelled as a mixed integer non-linear programming problem which is proved to be NP-hard. To solve this problem, a centralized (1 - ε)-optimal algorithm and an efficient distributed algorithm are provided. To evaluate the algorithm performance, the real-world traces are used to illustrate the effectiveness of our scheme.