In this article a generic method for fault detection and isolation (FDI) in manufacturing systems considered as discrete event systems (DES) is presented. The method uses an identified model of the closed-loop of plant and controller built on the basis of observed fault-free system behaviour. An identification algorithm known from literature is used to determine the fault detection model in form of a non-deterministic automaton. New results of how to parameterise this algorithm are reported. To assess the fault detection capability of an identified automaton, probabilistic measures are proposed. For fault isolation, the concept of residuals adapted for DES is used by defining appropriate set operations representing generic fault symptoms. The method is applied to a case study system.