In this paper, the problem of robust fault diagnosis of proton exchange mem- ments lie inside their corresponding estimated interval bounds. When a fault is detected, the measurements that are inconsistent with their corresponding estimations are annotated and a fault isolation procedure is triggered. By using the theoretical fault signature matrix (FSM), which summarizes the effects of the different faults on the available residuals, the fault is isolated by means of a logic reasoning that takes into account the bounded uncertainty, and if the number of candidate faults is more than one, a correlation analysis is used to obtain the most likely fault candidate. Finally, the proposed approach is tested using a PEM fuel cell case study proposed in the literature.