Tape virtualization systems' I/O performance have become almost the same as those observed in disk subsystems. However, few studies can be found in the literature on iSCSI performance with tape virtualization subsystems. Fibre Channel over Ethernet (FCoE) has been proposed recently as an alternative to both iSCSI and FC, but it remains challenging to find FCoE performance studies. Considering this gap in the literature, we did a comparative performance study between FCoE and iSCSI by executing I/O operations in virtual tapes using different block sizes. The goal was to determine the I/O average throughput, protocol overhead, I/O latency variance and relation between average throughput and CPU usage. The results showed an equivalent I/O throughput between FCoE and iSCSI operations, but FCoE surpassed iSCSI considering its lower overhead, processing and I/O latency variance values. It was also noted that FCoE software implementation must be enhanced.