Barcode and Radio Frequency Identification (RFID) as identification technologies are widely used in warehouses of the logistics supply chain to track and locate storage units, track manipulation equipment and the state of storage locations. Depending on the needs and design of the warehouse and the way its operations are executed, one identification system can be used more frequently than the other. The identification system influences how logistical processes in the warehouse are performed, and it is often integrated with some form of the Warehouse Management System (WMS). The correct choice of an identification system influences data accuracy, resource utilization, waiting times for process execution and overall efficiency. This paper aims to show specific differences in the use of barcode or RFID technology, on the example of the reference warehouse system. Two warehouse logistic processes (storing and issuing of products) are described and modelled with the BPMN, to define all the process elements. Then, process simulation models are created, and both barcode and RFID systems are tested in the process simulation experiments. The simulation results enable the comparison of key performance indicators, based on the required process and waiting time for checking goods which flow through the system and the utilization of the material handling equipment.