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Orthogonal netted radar systems (ONRS) can fundamentally improve radar performance by using a group of specially designed orthogonal signals. A novel hybrid algorithm is proposed to numerically optimize such orthogonal polyphase code sets. The proposed algorithm integrates a statistical simulated annealing algorithm with the traditional iterative code selection method and is demonstrated to be effective for the design of polyphase signals used in ONRS. Some of the design results are presented and discussed. The effect of Doppler frequency shift on the performance of the designed signals is also investigated.