Provided herein are methods and apparatus for a self-synchronizing software defined radio apparatus wherein the method includes instructing, by a leader module of an RF clock module of the software defined radio apparatus and via a controller module comprising a central coordinator operative to provide a data bridge, a radio frequency (RF) transceiver to transmit a two-tone frequency signal at f1 and f2 over air, separated by a desired input clock frequency, the RF transceiver operative to receive and transmit RF signals, receiving, at a follower module, a transmitted signal, extracting, by the follower module, an envelope of the received signal, and passing the received signal through a filter to obtain a reference clock without modifying existing physical/link layer protocols.