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Autonomous ships transferring valuable cargoes and humans in a more efficient and cost effective manner will soon be state of the art technology. Yet, their ICT system architecture and operations have not been defined in full detail. Moreover, multiple cyber security issues remain open and should be addressed. No study to date has analyzed fully the architecture of the autonomous ship, even less so have potential cyber threats and cyber attacks been identified. In this paper we identify and categorize systems that make up an autonomous ship, we propose a generic system architecture, and we analyze the cyber security of the ship by leveraging the STRIDE threat modeling methodology to identify potential cyber attacks, and to analyze the accordant risk. The results will support ship designers and industry towards improving the autonomous ship system architecture and making ship operations more secure.