As an important component of soil food web, gymnamoebae play a significant role in nutrient cycling and energy flows of terrestrial ecosystems by linking soil microorganisms and macro- and meso-fauna. Along an elevational gradient (700 m, 1,000 m, 1,300 m, 1,600 m, 1,900 m, 2,200 m) in Changbai Mountains, the community composition and structure of gymnamoebae were compared using most probable number (MPN) method and plate cultivation technique. The result suggested that gymnameobae richness differed significantly among the various elevational levels and was positively correlated with soil pH. The lowest richness was observed in an Betula ermanii forest with monospecies dominance (1,900 m), while the highest richness was observed in the 1,000 m ecotone. Shannon-Wiener diversity index and Pielou envenness index performed similar patterns with richness, with no significant differences observed among different elevational levels. The community composition of gymnamoebae was more similar among 1,300 m, 1,600 m and 1,900 m and between 2,200 m and 700 m elevations. Canonical correspondence analysis showed that gymnamoebae community structure was correlated with soil pH, ammonium nitrogen and C/N ratio. However, gymnamoebae communities were not influenced by altitude and soil water content. In conclusion, unlike macroorganisms (e.g. trees and animals), the richness and diversity of gymnamoebae did not show monotonically decreasing or hump-shaped patterns along the elevational gradient, and soil physicochemical characteristics were the main factors that influencing their distribution. In addition, gymnamoebae community composition and structure might be also indirectly regulated by vegetation type through litter and root exudates.