A control system of a robot cleaner including a signal transmitting unit and a cleaning unit is provided. The signal transmitting unit wirelessly transmits reference signals, while the cleaning unit receives the reference signals from the signal transmitting unit and performs cleaning while moving through a region to be cleaned set in accordance to the received reference signals. Accordingly, the present invention causes the robot cleaner to be efficient in cleaning a local region of a given large area and provides for convenient use of the robot cleaner.