Current variability at the Pacific entrance of the Indonesian Throughflow is investigated using direct current and hydrographic measurements. Two moorings with three current meters (depths of 350, 550, and 1050 m) and one conductivity-temperature-depth profiler (260 m) were deployed at 4 ¿1'N, 127 ¿31'E and 3 ¿11'N, 128 ¿27'E between Talaud Islands and Morotai Island (Indonesia) from February 1994 to June 1995. Data from four hydrographic surveys conducted mainly between Mindanao and New Guinea from 1994 to 1996 are also used. The onset of a strong northwestward flow was observed at the southern mooring during boreal winter. In contrast, a southwestward flow containing salty South Pacific water was observed there during boreal summer. This current pattern change matched monsoon change around the mooring sites, suggesting that this variability is a seasonal signal in this region. This current change may occur because of the meridional shift of the Halmahera Eddy associated with an enlargement/diminishment of the Mindanao Dome. Our observation result during summer (the southwestward flow with the South Pacific water at the southern mooring) suggests that the Maluku Sea is one of the eastern routes of the Indonesian Throughflow. The current data also revealed that intraseasonal variability occurs in 50-day oscillations. Because the coherence between wind variability in the tropics with a period of 40--50 days (Madden-Julian Oscillation) and current variability with this period are >0.4, it is possible that the 50-day oscillation in the ocean current is induced by wind variability associated with the Madden-Julian Oscillation. The ocean eddy activity with an intrinsic period in this region may also be related to this 50-day oscillation. ¿ 1999 American Geophysical Union