An encryption system has been provided to self-synchronously scramble communications where the receiver must recover the clock information from the data stream, such as the SONET format. To prevent jamming during initialization, or during times when no data is being transferred, flags and overhead data are scrambled, along with the payload. Timing controls to the scrambler permit this scrambler to be selectively engagable, so that the selective overhead scrambling becomes a second layer of scrambling. A method of self-synchronously scrambling the overhead in NRZ formatted communications is also provided.