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This paper describes the development of an acoustic probe designed to perform in-situ measurements of ferro-manganese crust thickness at depths of up to 3000 m. It is planned that this device will operate at low altitudes off the seafloor, mounted onboard an underwater vehicle, and continuously map the crust thickness of regions extending over several kilometres. A prototype probe has been developed together with an algorithm that automatically detects the reflections from the top and bottom surfaces of a layer of crust and measures its thickness. The performance of the system is demonstrated through a series of laboratory experiments carried out using crust samples obtained during the NT09-02 Leg 2 of the R/V Natsushima. First, the ability of the system to measure crust thickness at various ranges to the target is assessed. Next, the effects of pressure are investigated in an experiment where the thicknesses of several crust samples are measured at pressures between 0.1 and 30MPa. Finally, the sub-bottom profiles of a number of crust samples, with and without substrates attached are measured.