Even though Pacific - Indian Ocean exchange [Indonesian Throughflow (ITF)] has been measured for the last three decades, the measurements of microplastic in the region is very limited. This study was the initial investigation of the vertical distribution of microplastic in the deep-sea areas across the ITF Pathway. Niskin water samples were utilized to obtain the samples from a water column in a range of 5 to 2450 m. A total of 924 microplastic particles with an average abundance of 1.062 ± 0.646. n/L were found in the water column. Our findings indicate that water temperature and water density are the most significant factors correlated to the microplastic concentration. This study will be the first report discussing the distribution of microplastics in the deep-sea water column that could be highly significant in determining the fate and transport of microplastic within Indonesian waters that exits into the Indian Ocean.