The Changbai Mountains, recognized as one of the global biodiversity hotspots, remain underexplored in terms of chrysophycean stomatocysts, despite their rich biological diversity. This study investigated the diversity of chrysophycean stomatocysts in fifteen surface Sphagnum samples and thirteen peat core samples collected from Hani, Jinchuan, Gushantun and Yuanchi Peatlands of the Changbai Mountains, northeastern China. Sixty-eight morphotypes of stomatocysts were identified and described according to the International Statospore Working Group, with five new morphotypes. This is the first record of chrysophycean stomatocysts in the Changbai Mountains, highlighting rich morphotypes of stomatocysts in these temperate peatlands, and hence the results can improve our knowledge on the diversity of stomatocysts in the temperate monsoon regions and create a taxonomical basis for further stomatocyst-based environmental monitoring and paleoenvironmental studies.