A method and system for efficiently merging subnets having individual subnet managers (SM) into a single network with one master SM. During discovery and configuration of a subnet, a subnet manager creates a Subnet Management Database (SMDB) representative of the subnet components being managed. Each subnet manager contains an independent SMDB. When two or more subnets are linked/connected together to form a single network, a single one of the subnet managers is selected as the master subnet manager and all the subnets' SMDBs must be merged. An SMDB record labeling mechanism is utilized to differentiate among components from the different subnets that may have the same parameter values, such as protection keys (P_keys) and re-assign individual parameters to create a single SMDB of uniquely defined components.