Given the different configurations for SAS and SATA Host and Target Ports, embodiments of the present invention automatically detect the configuration of SATA and SAS Phys when any device is inserted into a port enclosure and properly configure the connection regardless of the Phy configuration of the connected device. When a device is connected to the system, the port listens for either a SATA or SAS OOB signal to determine if the receive pin of the port is properly connected to the transmit signal of the attached device. By switching the configuration periodically and listening for the OOB signal, the port can determine which configuration is proper. Once a signal is detected, the port can properly configure the connection and continue with the SATA or SAS insertion algorithm. A user may alternatively choose which configuration to use and bypass the automatic detection and configuration.