In multi-hop relaying systems that have many relay stations (RSs), a cognitive radio (CR) technique can improve system performance greatly, due to an efficient resource sharing between the RSs. In this letter, the performance of an ARQ mechanism for CR-based multi-hop relaying systems is studied, using Markov chain and matrix signal flow graph (MSFG) techniques. Also, a priority-based resource allocation scheme is proposed to prevent performance degradation caused by the usage of unstable resources acquired by the CR technique.