The improved genetic algorithm was applied to the optimization design of high performance millimeter wave diplexers. The waveguide H plane junctions and the E plane septum filters were used for designing the diplexers. The genetic algorithm was used to optimize the diplexer including optimizing the filters and the structural parameters of the diplexer itself. Three diplexers of different frequency bands were designed accoding to this method.One diplexer of millimeter wave band was designed and fabricated. The agreement between the theoretical and the experimental results of a millimeter wave diplexer proved the accuracy and validity of the genetic algorithm.