Abstract The myxomycetes are a group of protists that form a monophyletic taxon in the phylum Amoebozoa. Evidence of their evolutionary success is the fact that they account for more species (ca. 900 are currently recognized) than the combined total for the rest of the Amoebozoa. Moreover, myxomycetes are present in every terrestrial environment investigated to date and also, as amoebae or flagellated cells, in aquatic environments where they cannot form fruiting bodies. Even if culture-based methods tend to underestimate their occurrence in soil, myxomycetes probably account for ∼50% of soil amoebae. The emergence of molecular-based methods has revolutionized our concepts of biodiversity, but myxomycetes are conspicuously absent from all environmental surveys. Herein we show that this is due to their highly diverging SSU rRNA gene sequences, which contain numerous Group I introns. Further proof comes from a recent study that used a massive sequencing approach without primer bias to amplify RNAs. The results obtained show that the mycetozoans (myxomycetes along with dictyostelids and protostelids) are indeed a dominant group of soil protozoans.