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In a conventional distribution system, protection algorithms are designed to operate on a unidirectional high fault-current level. In a microgrid, a fault current from distributed generation (DG) may bring about a relay malfunction because of the bidirectional and relatively small fault current. Therefore, the conventional protection scheme is not applicable to microgrids and a new protection method must be developed. In this paper, two protection coordination algorithms which can be applied for facility and secondary microgrids are proposed, respectively. The proposed protection algorithms eliminate faults not by the EMS signal but by directional relays. Moreover, this makes the algorithms flexible regardless of the types and numbers of DG. The proposed protection algorithms were simulated at the KEPCO RI Microgrid Demonstration Site.