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Recent mooring observations of ocean temperature provide the first high resolution, long term record of temperature variability in the Makassar Strait of the Indonesian Seas. The mooring observations span the entire cycle of the strong 1997/1998 El Niño. A high correlation (r = 0.67) is found between variability in the average thermocline temperature, to variability in the southward Makassar volume transport: during high (low) volume transport, the average temperature of the thermocline is also high (low). In addition, from nearly 15 years of XBT data, the Makassar thermocline temperature is shown to be highly correlated (r = 0.77) to SOI. This reveals that the Makassar temperature field–when coupled with the throughflow–transmits the equatorial Pacific El Niño and La Niña temperature fluctuations into the Indian Ocean. The ENSO variability in the internal energy transport is calculated: 0.63 PW during the La Niña months of December 1996 through February 1997, and 0.39 PW during the El Niño months of December 1997 through February 1998.