The second MAGIC telescope, a clone of the first 17 m diameter MAGIC telescope, has entered the final commissioning phase and will soon start to take data, preferentially in the so-called stereo-mode. The control system for both telescopes is assigned to a number of autonomous functional units called subsystems. The control hardware and software components of the second telescope subsystems have been modified with respect to their counterparts of the first telescope. A new Central Control (CC) program has been developed to communicate with all the subsystems of both telescopes and to coordinate their functionality thus easing the stereo data taking procedure. We describe the whole control system in detail: all the subsystems and their communication with the Central Control, the CC graphic user interface that grants operators the full control over the two telescopes, and the automatic checking procedures, which guarantee the safety and 'health' of the apparatus.