The diversity of eukaryotic macroorganisms such as animals and plants usually declines with increasing elevation and latitude. By contrast, the community structure of prokaryotes such as soil bacteria does not generally correlate with elevation or latitude, suggesting that differences in fundamental cell biology and/or body size strongly influence diversity patterns. To distinguish the influences of these two factors, soil eukaryotic microorganism community structure was investigated in six representative vegetation sites along an elevational gradient from forest to alpine tundra on Changbai Mountain in Northeast China, and compared with our previous determination of soil bacterial community structure along the same gradient. Using bar-coded pyrosequencing, we found strong site differences in eukaryotic microbial community composition. However, diversity of the total eukaryotic microorganism community (or just the fungi or protists alone) did not correlate with elevation. Instead, the patterns of diversity and composition in the total eukaryotic microbial community (and in the protist community alone) were closely correlated with soil pH, suggesting that just as for bacteria, acidity is a particularly important determinant of eukaryotic microbial distributions. By contrast, as expected, plant diversity at the same sites declined along our elevational gradient. These results together suggest that elevational diversity patterns exhibited by eukaryotic microorganisms are fundamentally different from those of plants.