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This paper describes acoustic and visual instruments developed to perform high-resolution surveys of the volumetric distribution of manganese crusts from an underwater vehicle. The instruments consist of an acoustic device, developed to perform in situ measurements of manganese crust thickness at depths of up to 3000 m, and a vision-based mapping system that generates 3-D color reconstructions of the seafloor. Methods to process the information obtained by these sensors to automatically identify areas of exposed crust using the 3-D reconstructions, and subsequently determine the thickness of the crusts based on the acoustic measurements, are described. Sea trials were performed at #5 Takuyo seamount with the systems mounted onboard the remotely operated vehicle Hyper-Dolphin during the NT10-11 cruise of the R/V Natsushima. The results are that the first time in situ measurements of manganese crust thickness have been performed, and it is demonstrated that, for the types of substrate dominant in the surveyed area, continuous acoustic measurement of manganese crust thickness is possible. The work described in this paper indicates that the proposed instruments and data processing algorithms can form useful tools to enable more efficient survey of manganese crusts.