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Semantic communication, emerging as a breakthrough beyond the classical Shannon paradigm, aims to convey the essential meaning of source data rather than merely focusing on precise yet content-agnostic bit transmission. By interconnecting diverse intelligent agents (e.g., autonomous vehicles and VR devices) via semantic communications, the semantic communication networks (SemComNet) supports semantic-oriented transmission, efficient spectrum utilization, and flexible networking among collaborative agents. Consequently, SemComNet stands out for enabling ever-increasing intelligent applications, such as autonomous driving and Metaverse. However, being built on a variety of cutting-edge technologies including AI and knowledge graphs, SemComNet introduces diverse brand-new and unexpected threats, which pose obstacles to its widespread development. Besides, due to the intrinsic characteristics of SemComNet in terms of heterogeneous components, autonomous intelligence, and large-scale structure, a series of critical challenges emerge in securing SemComNet. In this paper, we provide a comprehensive and up-to-date survey of SemComNet from its fundamentals, security, and privacy aspects. Specifically, we first introduce a novel three-layer architecture of SemComNet for multi-agent interaction, which comprises the control layer, semantic transmission layer, and cognitive sensing layer. Then, we discuss its working modes and enabling technologies. Afterward, based on the layered architecture of SemComNet, we outline a taxonomy of security and privacy threats, while discussing state-of-the-art defense …