Most of previous genetic algorithms for solving graph problems have used a vertex-based encoding. We proposed an edge encoding based new genetic algorithm using a spanning tree. Contrary to general edge-based encoding, a spanning tree-based encoding represents only feasible partitions. As a target problem, we adopted the MAX CUT problem, which is well known as a representative NP-hard problem, and examined the performance of the proposed genetic algorithm. The experiments on benchmark graphs are executed and compared with vertex-based encoding. Performance improvements of the spanning tree-based encoding on sparse graphs was observed.