The article presents the process of creating an example multi-domain Software Defined Network based on open source solutions. Significant threats to the SDN and currently used protection practices were discussed. Authors proposed a solution to the problem of resource authorization and authentication by introducing a Hidden Data Layer based on steganographic methods to SDN. Hidden Data Layer consists of three essential elements, i.e. a Head Resident which doubles the functions of a public SDN controller and is a superior unit concerning public one, a Hidden Layer Protocol realising communication between individual network elements. The third element is Hidden Protocol Interpreter as an interpretive and executive function which carries out tasks sent by secret layer protocol. This type of solution assures at first fast and effective detection of threats and secondarily redundancy of the control layer in the case of disabling or debilitating the use of the public controller.