At sites 89 and 90 of the Korea Deep Ocean Study (KODOS), located in the western part of the area between the Clarion and Clipperton fracture zones, the topmost sediment column can be divided into two layers by a sharp color boundary: an upper pale brown layer (Unit A) and a lower dark brown layer (Unit B). Geochemical and mineralogical properties in Units A and B are clearly different across the color boundary, which can be interpreted to be a hiatus with an age gap of at least 3 Ma. The large gap in sediment ages results in an overall difference in sediment properties between Units A and B. That is, older Unit B sediment is higher in smectite contents, more severe in fossil dissolution, and lower in POC contents, commonly due to prolonged diagenesis. Disappearance of the coarse mode (50–60 μm) of the size distribution in Unit B is a result of prolonged dissolution of siliceous fossils. However, other phenomena occurring just below the color boundary (the most severe dissolution of fossils, the most frequent occurrence of coarse-grained micronodules and smectite aggregates, maximum value of metals (Mn, Cu, Ni), and increased water contents) can be explained by the active stirring of bottom sediments by intensified paleo-bottom currents present during the hiatus. That is, turbulence as well as winnowing action caused by the paleo-currents had, respectively, accelerated the dissolution of siliceous fossils and the concentration of coarse grains at the hiatus. In addition, micronodule formation was promoted by the efficient formation of oxygen-depleted micro-environments around in-situ fauna remains, which were buried efficiently by increased reworking and resedimentation of bottom sediments by the paleo-current activity. Meanwhile, increases in metal and water contents just below the color boundary are the results of the concentration of micronodules enriched in metals and probable formation of ‘woodpile’ fabric by abundant spicules and spines, respectively. Active stirring of bottom sediments by the intensified paleo-bottom currents as well as the large gap in sediment age between Units A and B are mostly responsible for the vertical variations of geochemical and mineralogical properties in two-color core sediments.