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The characterization of specific subsets of soil microbiota in the rhizosphere and endosphere has led to the recognition of plant species-specific microbiomes. Most attention has been given to microbial prokaryotes and fungi. Only recently was convincing evidence for the existence of plant species-specific protist microbiomes presented. Although protists are expected to shape the composition of bacterial and fungal communities and, thereby, directly impact plant health, a lack of cultures of these important plant-symbiotic protists has hampered their experimental exploration. To facilitate empirical plant microbiome research, we sampled Arabidopsis thaliana, established 79 cultures covering nearly all major groups of plant-symbiotic Cercozoa (protists), and have made these publicly available. We discuss our findings and propose potential roles that these protists may have in structuring the plant microbiome.