With the increasing interest in Semantic Web-based applications, researchers have started to build tools enabling organisations to share information. An important aspect in maintaining the Semantic Web is, however, to preserve security during semantic interoperation of different entities. Security and privacy are indispensable to the success of Semantic Web services. Hence, this chapter aims to investigate the currently used security methods in semantic interoperation, including the security methods employing Semantic Web representation languages such as XML, RDF and ontologies, and their application methods in semantic interoperation such as secure access control and secure knowledge management. How to manage privacy, trust and reputation at the same time during semantic interoperation will also be discussed in this chapter. Finally, some directions for our further research will be presented.