A method for determining a slave clock to master clock time difference with an alignment marker. The method selects and transmits a first alignment marker at a first time by a transmitter that has a master clock in a first message to a receiver that has a slave clock. Subsequent to transmitting the first message, the method further transmits a second message that contains the first time and an identity of the first alignment marker. The method further receives the first message and records a second time that the first message is received. The method further receives the second message and the first time and the identity of the first alignment marker. The method further determines a transmission delay and generates a time difference from the slave clock to the master clock.