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The goals of this article are twofold. First, we detail the operations and discuss the results of the 2005 Chios ancient shipwreck survey. This survey was conducted by an international team of engineers, archaeologists, and natural scientists off the Greek island of Chios in the northeastern Aegean Sea using an autonomous underwater vehicle (AUV) built specifically for high‐resolution site inspection and characterization. Second, using the survey operations as context, we identify the specific challenges of adapting AUV technology for deep water archaeology and describe how our team addressed these challenges during the Chios expedition. After identifying the state of the art in robotic tools for deep water archaeology, we discuss opportunities in which new developments and research (e.g., AUV platforms, underwater imaging, remote sensing, and navigation techniques) will improve the rapid assessment of deep …