Based on both major and trace element chemistry, the occurrence of the intergranular component in mantle-derived xenoliths from far eastern Russia has been constrained. Whole-rock trace element measurements of one xenolith show apparent negative anomalies in Ce, Th, and high field strength elements on normalized trace element patterns. The trace element pattern of the whole rock differs from those of constituent minerals, indicating that the anomalies in the whole rock are attributable to the presence of an intergranular component. That assumption was confirmed using in situ analysis of trace elements in the intergranular substance and melt inclusion using laser ablation inductively coupled plasma–mass spectrometry. Both the intergranular component and the melt inclusions have identical trace element patterns, which mean that these materials are a cognate metasomatizing agent. The anomalies are regarded as mantle metasomatism related to an aqueous fluid. Hydrous minerals were observed on the wall of the melt inclusions using micro-Raman spectroscopy, indicating that the melt inclusions contained a large amount of water. Thus, this study reveals a trace element composition of a hydrous metasomatizing agent in the mantle.