This paper proposes a method to design optimally tuned fractional order as well as integer order proportionalintegral-derivative (PID) controllers for twin rotor-multi-input multi-output system (TRMS). Two fractional order PID (FOPID) controllers for one degree of freedom (1-DOF) in horizontal plane and 1-DOF in vertical plane are designed separately using linear model. Design criterion consists of a performance index which is minimized using particle swarm optimization (PSO) to obtain the controller parameters for satisfactory responses. In order to assess the performance of closed loop control system a continuously varying reference trajectory has been taken which is tracked by actual response. It is found in simulation study that the FOPID controllers perform better than integer order PID (IOPID) controllers based on same design criteria.Index Terms-Twin rotor MIMO system, FOPID, IOPID, particle swarm optimization, performance index.