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Makassar strait as the main entrance of the Indonesian Through low (ITF) known to carry the ITF transport about 75% of 15 Sv total transport. Current mooring measurement in Labani Channel has been made since 1996, however, the hidrography measurement that covering the entire Makassar Strait is still rarely done. The canal countour and bathymetry diversity of the strait affect the characteristic of mass water moving so that the research which cover the entire of the Makassar Srait is needed. The aims of this study were to investigated the current structure and spatial variation of ITF in Makassar Strait from EWIN expedition during June 2013. Hidrographic data consists of 29 CTD casts that distributed over the Makassar Strait waters and current data was from shipboard ADCP along the survey path at 0-125 m. The result showed that ITF of Makassar Strait was characterized by a strong jet current that intensive in thermocline depth (75-125 m), where the flow pattern toward the south to southwest at the entrance of ITF in the northern. The jet current continues to approach the 2°S, then the direction changed to southeast down the shallow Kalimantan slope to Labani Channel and become stronger. In the edge of Makassar Strait, circulation form cyclone eddies. ITF waters stratification was dominated by North Pacific Subtropical Water (NPSW) in the thermocline depth and North Pacific Intermediate Water (NPIW) in the below of thermocline depth. There was spatial variation of mass water NPSW and NPIW where ITF weakness toward southern with decreaces 0.03 psu of maximum salinity and increaces 0.007 psu of minimum salinity. Thermocline layer in the eastern was thicker so that the vertical distribution of mass water of North Pasific was likely stronger in the east side of Makassar Strait. [ABSTRACT FROM AUTHOR]