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Integration of fuel cell Auxiliary Power Units (APUs) into vehicles requires that the vehicle Electronic Control Unit (ECU) communicate with the fuel cell controller using appropriate protocol. The common communication standard used in automotive systems is the CAN protocol. Some fuel cell controllers originate from stationary power scenarios and communicate using process industry communication protocols such as MODBUS. This paper reviews the MODBUS TCP protocol and CAN protocol. It then describes the MODBUS TCP software driver development for QNX Real Time Operating System (RTOS) used in the SwRI® Rapid Prototyping Electronic Control System (RPECS). The architecture of the communication system on the vehicle and details of RPECS needed to understand the MODBUS drivers are described. Tools such as RPECS™ and EtherPeek™ (TCP/IP packet sniffing software) used during debugging are also briefly described. A new mapping method for conversion between MODBUS and CAN protocols is proposed.