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This study describes the optimal generator tripping planning for special protection system (SPS) in an independent power system. This SPS is dealing with the transient instability caused by transmission line N-3 contingencies. The immune algorithm is adopted to select the tripping generators in order to keep power system stable. Taiwan power system is the base power flow case for simulation. The optimization result is verified with PSS/E and PEALS programs. The verification shows the optimal generator tripping selection in this SPS. The proposed algorithm provides a valuable reference in the development of an SPS for similar independent power systems.