GTPases of the Ras superfamily are a vast group of proteins crucial for many eukaryote-specific cellular processes. Virtually nothing is known about these proteins in Microsporidia, a group of intracellular parasites with extremely divergent genomes. We carefully scrutinised genome sequences from 22 microsporidian taxa and eventually detected 16 different groups of orthologs belonging to the superfamily. However, many of the individual genes are extremely divergent and their recognition was possible only thanks to the broad sampling of microsporidial genomes and/or application of sensitive homology search methods. Assigning the microsporidial Ras superfamily members to orthology groups in other eukaryotes proved to be another challenge defying standard phylogenetic analyses, but the genome of the recently described, less divergent microsporidial relative, Mitosporidium daphniae, turned out to be a helpful bridge between genes in microsporidia and ?canonical? eukaryotes.