We investigated fossil planktonic foraminifera from cores ND-02 (Nakdong River delta) and PC-11 (inner shelf off southeast Korea), to assess millennial-scale variations in the surface oceanography. The coiling ratio of Neogloboquadrina pachyderma shows five millennial-scale near-cyclic fluctuations (~8.7–8.3, ~7.5–6.2, ~4.7, ~2.8 and ~0.5 ka) since ~9 ka. These variations are similar to warm-water diatom variations at the Oki Ridge where a cyclicity of ~1.6 kyr is present, possibly associated with a Bond event. By contrast, the near-cyclic variations in our planktonic foraminiferal record were not fully consistent with the intensity variations of the Tsushima Warm Current and Kuroshio current. Our records from southeast Korea seem to reflect the more regional oceanographic variations in the marginal seas of East Asia. We suggest that the coastal upwelling of the subsurface water along the southeast coast of Korea plays an important role in generating near-cyclic variations of warm-water biota, with a possible connection to a Bond event.