Late Quaternary foraminifera assemblages have been examined in two sediment cores (MD179‐3296 and MD179‐3317) from cold seep areas in the eastern margin of the Japan Sea, off Joetsu, Niigata Prefecture. Foraminifera assemblages in core MD179‐3296, which was located at the center of a pockmark on the Umitake Spur, show no evidence of methane flux and, especially in its upper portion, share the same paleo‐environmental history as other free gas hydrate areas of the Japan Sea. In comparison, in the core MD179‐3317 at the center of a pockmark at Joetsu Knoll, foraminiferal distributions were strongly affected by methane activities and, in the main part of the core, were deposited under local conditions. Three horizons were identified in this core, which are characterized by the high abundance value of Thalmannammina parkerae and might be related to methane flux due to sea level fall especially through late marine isotope stage (MIS) 3 and MIS 2.