The aim of software module clustering problems (SMCPs) is to automatically find a good quality clustering of software modules based on relationships among modules. In this paper, we propose a multi-agent evolutionary algorithm to solve this problem, labeled as MAEA-SMCPs. With the intrinsic properties of SMCPs in mind, three evolutionary operators are designed for agents to realize the purpose of competition, cooperation, and self-learning. In the experiments, practical problems are used to validate the performance of MAEA-SMCPs. The results show that MAEA-SMCPs can find clusters with high quality and small deviations. The comparison results also show that MAEA-SMCPs outperforms two existing multi-objective algorithms, namely MCA and ECA, and two existing single-objective algorithms, namely GGA and GNE, in terms of MQ.