Microsporidia cause important diseases in aquatic organisms. Susceptible hosts span a remarkable taxonomic spectrum, from protists to mammals. Known genera represent a small fraction of extant taxa in global aquatic systems. Transmitting horizontally or vertically, effects range from cryptic to catastrophic; individual level effects being extrapolated to populations and ecosystems. Debate over positioning within the eukaryotes and internal structuring of the phylum has benefited from molecular phylogenetic approaches to taxonomy. Similar tools offer new perspectives on transmission between hosts of differing trophic status and habitats. Accessible models for host-pathogen interaction are emerging from full genome sequencing projects. Hyperparasitism and the close phylogenetic relationship between taxa infecting invertebrates and vertebrates not only underline a ubiquity in aquatic systems but also potential for zoonotic transfer.