Control plane management based on physical topology of nodes in software-defined networks (SDNs) is provided. Nodes in an SDN are organized into a plurality of node clusters. A cluster of nodes in an SDN is formed and control plane management for the nodes within the cluster is provided. A topology-aware assignment of nodes to controllers in an SDN is provided. Related nodes such as root and corresponding child nodes are assigned to a single cluster in one embodiment to lessen the impacts of controller failure. The assignment of nodes to controllers is also provided based on minimizing traffic between node clusters and between nodes and external networks.