This paper presents the Artificial Bee Colony (ABC) optimization algorithm with application to flexible manipulator system (FMS). The aim of the algorithm is to find the best possible tuning parameter that can provide accurate angle trajectory of FMS. Five performance criteria havebeen used as an objective function of this problem where several conditionswith different ABC parameters settingare set to determine which performance criteria is most suitable intuningthe PID controller in order toobtain the best FMS performance.The results show that the ABC withRoot Mean Square Error (RMSE)as performance criteria outperforms the ABC with other performance criteria and it able to tune the PID controller of FMS to the desired hub angle trajectory.