Reconfiguration of microgrid results in dynamic variation in topology of the network. Due to this, the conventional protection scheme is no longer applicable in microgrid. Hence the microgrid network demands an adaptive protection scheme, which is a key challenge to protection engineers. It is critical for the protection engineers to know the current topology of the microgrid before a suitable relay coordination technique is deployed on it. This paper proposes a Prims aided Floyd Warshall algorithm, where the Prims algorithm identifies the current topology of the network at any instant of time. In the event of fault occurrence, the output of Prims algorithm is a list of active nodes: utility grid, loads, Distributed Generators (DG) and critical circuit breakers in the network. This list aids the Floyd Warshall algorithm in identifying the shortest path from the node closer to the fault to the utility grid (in grid connected mode) or point of common coupling (in islanded mode). The algorithm ensures minimum portion of network disconnection for fault isolation. The proposed algorithm is tested and validated on an IEEE 21-bus microgrid network in islanded mode and an IEEE 69-bus distribution network with DG included at certain nodes in grid connected mode. © Springer Science+Business Media Singapore 2017.