A method and system for controller level identification and isolation of a degraded physical link (PHY) in a serial attached small computer system interface (SA-SCSI) or SAS domain. The method and system uses computer readable code embodied within the controller level of an SAS domain to monitor a plurality of PHY pairs associated as connecting through a wide port. The invention compares a history of PHY pair errors to a tunable timer to determine if PHY errors reach a threshold. Should the threshold be exceeded, the controller disables the error prone PHY pair and delivers a notification. The controller may then re-enable the disabled PHY after user action or port power up.