A protocol independent multiplexer is described that allows for multiple different protocols that operate at different bit rates to be combined and output in a format that may have yet another bit rate. The multiplexer includes a series of inputting devices that are each coupled to a respective buffering device, a mapping device coupled to each of the buffering devices, and an outputting device coupled to the mapping device. Each of the inputting devices receive an input optical signal and forwards recovered data information to the corresponding buffering device. The buffering devices store the data information and output to the mapping device, the outputting being controlled by the mapping device to ensure that the buffering devices remain approximately half full. The mapping device formats the data information into individual data units and outputs the data units to the outputting device which subsequently multiplexes the data units. One key advantage of this protocol independent multiplexer is that only one piece of hardware is required for the operation of numerous different protocols.