Generally, in MVDC shipboard micogrid system, all the loads, and sources are connected to centralized MVDC bus through suitable power electronic converters. These power electronic converters are of two port structure and are used to control the parameters of MVDC bus, source, and load. If any fault occurs on source/sink connection or MVDC bus, results in the isolation of source/sink from the MVDC bus or total shutdown of the MVDC system. This decreases the performance of the shipboard sub-systems. For providing the uninterrupted power supply problem during faults, this paper presents a new fault tolerant two layer shipboard microgrid architecture for next generation electric ships. This two layered microgrid architecture has one MVDC bus and one MVAC bus, which are connected through interlinking converter. And, all the electrical equipment (sources/sinks) are connected to both MVDC/MVAC buses through a three port converter (TPC). In normal operation of TPC, sources/sinks are connected to its respective bus. And, if any fault will occur on any of the buses, TPC shifts its source/sink of the faulted bus to un-faulted bus. The fault tolerant two layer microgrid system was simulated using MATLAB/Simulink. The comparative results shows the effectiveness of the proposed architecture.