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Service Oriented Architecture (SOA) is considered as a standard for enterprise software development. The main characteristics of SOA are dynamic discovery and composition of software services in a heterogeneous environment. These properties pose newer challenges in fault management of SOA-based systems (SBS). A proper understanding of different faults in an SBS is very necessary for effective fault handling. A comprehensive three-fold fault taxonomy is presented here that covers distributed, SOA specific and non-functional faults in a holistic manner. A comprehensive fault taxonomy is a key starting point for providing techniques and methods for accessing the quality of a given system. In this paper, an attempt has been made to outline several SBSs faults into a well-structured taxonomy that may assist developers to plan suitable fault repairing strategies. Some commonly emphasized fault recovery strategies are also discussed. Some challenges that may occur during fault handling of SBSs are also mentioned.