Recent reviews have pointed out the large proportion of microbial eukaryotic (protist) diversity that has yet to be described, and the enormous challenges that accompany its description [1]. The ∼100 000 species [2] of microbial eukaryotes may be significantly underestimated if we continue to discover increasing numbers of cryptic species. Tools such as environmental sequencing, which have been highly successful in revealing novel lineages of uncultured bacteria and archaea, promise to add substantial new data for comparatively little effort [1].