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In addition to the dynamic nature of microgrids, uncertainty in the proper operation of protection system and communication links are other challenges affecting the protection coordination of these networks. Therefore, in this paper, a new protection coordination plan based on decision tree for considering uncertainties in the topology of microgrid, protection system, and communication links is presented. The proposed method allows the adaptive protection to make global decisions and adopt the best strategy to clear faults depending on considered uncertainties. Since circuit breakers are the most prone to failure equipment in the protection system due to fault-caused stress, this paper models uncertainty in the protection system with uncertainty in the performance of circuit breakers. In order to consider uncertainty in circuit breakers and communication links, their probability of correct operation are not considered fixed but variable, respectively, proportional to the fault current flowing through the circuit breakers and the latency of communication links. The proposed plan was tested on a sample microgrid in DIgSILENT Power Factory. Results prove that using the proposed method, adaptive protection can establish an optimal sequence of strategies so that with the failure of each strategy, the best backup strategy is replaced given the uncertainties. [ABSTRACT FROM AUTHOR]