The entire FCoE fabric is a single virtual domain, even though there may be multiple FCFs and FDFs. The virtual domain is a different Domain_ID than any of the FCFs. In certain embodiments there are multiple FCFs, of which one is selected as the master or designated FCF. The master FCF performs normal fabric configuration in conjunction with the Fiber Channel fabric. The master FCF assigns the virtual domain FC node IDs and controls development of subdomain IDs. Virtual links are instantiated between the master FCF and other FCFs, between top level FDFs and the FCFs and between the FDFs at each of various levels. FDFs connected to ENodes proxy the master FCF for most FIP operations. FIP FLOGI and FDISC operations are handled by the master FDF, but the FDFs convert the FIP FLOGI requests to VD_FLOGI requests, which include information about the FDF handling the transaction.