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The Okinawa Trough (OT) in the East Asian continental margin is characterized by thick terrigenous sediment and ubiquitous volcanic-hydrothermal activities. In this study, the clays collected during IODP Expedition 331 to the middle OT (Iheya North Knoll) were analyzed for mineralogical and geochemical compositions. By comparing with the clays from the East China Sea shelf and surrounding rivers, we examine different clay origins. The hydrothermal field in the mid-OT is dominated by Mg-rich chlorite, while the recharge zone has clay mineral assemblages similar to the shelf and rivers, showing high content of illite, subordinate chlorite and kaolinite and scarce smectite. Compared to the terrigenous clays, the hydrothermal clays in the OT have high concentrations of Mg, Mn and Zr but low Fe, Na, K, Ca, Ba, Sr, P, Sc and Ti, while the hydrothermal clays in the mid-ocean ridge are relatively enriched in Fe and V and depleted in Al, Mg, Zr, Sc and Ti. Different fractionation patterns of rare earth elements also register in the terrigenous and hydrothermal clays, diagnostic of variable clay origins. We infer that the OT hydrothermal clay was primarily formed by the chemical alteration of detrital sediments subject to the hydrothermal fluids. The remarkably different compositions of hydrothermal clays between the sediment-rich back arc basin like OT and the sediment-starved ocean ridge suggest different physical and chemical processes of hydrothermal fluids and fluid-rock/sediment reactions under various geologic settings.