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This paper presents an advanced protection system design for the main power system of an all-electric ship. Considering the unique characteristics of shipboard power systems, current differential scheme has been chosen as the most reliable primary protection scheme. A graph-theory-based algorithm automatically assigns input currents to their proper differential protection zone. Based on these assignments, the protection scheme trips the minimal number of breakers to isolate a fault. This connection between the graph-theory algorithm and breaker assignments enables the protection system to be adaptive with different configurations. As an extension to these fast fault detection and isolation functions, the fast reconfiguration algorithm is developed to maintain the power balance of the remainder power system after a severe fault with the aim of reducing the impact of fault to the minimum.