Abstract
Summary Fungi are everywhere and interact with humans in countless ways, but a large group of fungi called ‘Cryptomycota’ has escaped detection until very recently. Still, the extent of diversity and ecological habits of this group remain largely unknown. We interrogated publically available 18 S rRNA gene datasets, obtained via high‐throughput sequencing from marine and freshwater samples, for C ryptomycota sequences. Contrary to previous work, we found evidence of substantial C ryptomycota diversity in the marine upper water column. Additionally, we produced a sequencing set from a groundwater aquifer, an environment unrepresented among 18 S rRNA gene pyrosequencing sets. The C ryptomycota community in this aquifer sample appears distinct from the community in both freshwater and marine environments with evidence of a unique aquifer clade. This study significantly expands the boundary of known C ryptomycota sequence diversity and characterizes the phylogenetic distribution of this diversity in aquatic environments. Furthermore, the approach utilized is generalizable to discovery of novel micro‐eukaryotic diversity from any lineage.