We report helium isotope data collected in the central Indian Ocean, from the Arabian Sea to the Southern Ocean, during a Japanese GEOTRACES cruise in 2009-2010. We found hydrothermal helium-3 plumes and confirmed that 3He/4He ratio anomalies were almost the same as those observed in WOCE cruises conducted in 1990s, which indicates the hydrothermal activity and abyssal currents have not changed largely for the last few decades.Maximum d3He value over 14% was observed at mid-depth (2000–3000 m) in the northern part (north of 30˚S) in the central Indian Ocean, whereas lower d3He was found in the southern part at the same depth, where d3He is defined as the percent deviation of the helium isotopic ratio relative to the atmospheric standard. The vertical distribution of d3He shows a similar trend with dissolved iron and manganese distributions in the hydrothermal plume. Lateral d3He distribution at mid-depth using our GEOTRACES data together with WOCE data suggest that the helium-3 plume in the central Indian Ocean derived from the Central Indian Ridge around 20˚S. It does not flow northward along the ridge but flows eastward as previously reported. The source of the helium-3 plume observed in the region adjacent to the Indian subcontinent might be in the Gulf of Aden as inferred from water properties. The d3He distribution could reveal clockwise deep-water circulation in the Arabian Sea.