A vertical pattern of fractionated polycyclic aromatic hydrocarbons (PAH) was studied in the Japan Basin in the Sea of Japan. The highest PAH concentration was found in the mesopelagic realm, possibly resulting from deep convection and/or subduction of intermediate water and its biogeochemical setting in the western Japan Basin. Using 226Ra and 228Ra as tracers revealed the PAH load in the open sea from the coastal polluted water. Dissolved PAHs (DPAH, fraction < 0.5 µm) were significantly prevalent particulate PAHs (PPAH, fraction > 0.5 µm) at all depths, associated with a predominance of dissolved organic carbon (DOC) over particulate organic carbon (POC). Hydrophobicity was more important for higher-molecular-weight PAHs to be distributed between particles and the solution, while the high Koc of low-molecular-weight PAHs indicated that their partitioning was driven by other factors, such as adsorbing of soot particles. PPAH and DPAH profiles differed from the POC and DOC profiles; nevertheless, a positive moderate correlation was found for DPAH and DOC for depths below the epipelagic, suggesting the similarity of the mechanisms of input of dissolved organic matter and DPAH into the deep interior of the Sea of Japan. The PAH flux calculations showed that biological pumps and overturning circulation contribute almost equally to removing PAHs from the bathypelagic waters of the Japan Basin.