Animal and plant richness in tropical rainforests have long intrigued naturalist. More recent work has revealed that parasites contribute to high tropical tree diversity and that arthropods are the most diverse eukaryotes in these forests. It is unknown if similar patterns are reflected at the microbial scale with unicellular eukaryotes or protists. Here we show, using environmental metabarcoding and a novel phylogeny-aware cleaning step, that protists inhabiting Neotropical rainforest soils are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific protist parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, we found too few Oomycota to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that microbes play a large role in tropical terrestrial ecosystems long viewed as being dominated by macro-organisms.