We have performed PIXE analysis of kuroko-type ore from the JADE hydrothermal site of the Okinawa Trough, Japan using the proton microprobe (PIXEPROBE). We analysed five kinds of ores dredged from the sea floor: (I) barite ore with small sulfide dissemination; (2) sphalerite-pyrite chimney; (3) pyrite ore; (4) sulfide veinlets in strongly altered rock; and (5) pyrite megacrystals in strongly altered rock. The analyses revealed that the trace element distribution is regulated by the occurrence mode of the ore, and within each ore, by the crystal structure. The distribution suggests that the hydrothermal system for kuroko ore formation is quite heterogeneous and its chemistry is controlled by local factors such as difference in temperature, and that in-situ PIXE analyses are essential for effective beneficiation strategy for the rare-metals from kuroko-type ore. (authors). 10 refs., 1 tab.