This chapter illustrates the current state-of-art with aquatic invertebrate microsporidiology and future research potential in this important pathogen group. Early work in the field of aquatic invertebrate microsporidiology focused on host species which were presumably relatively accessible via standard fieldwork operations. With the development of systematic approaches to pathology and the increasing access by researchers to samples from wider aquatic environments, an ever-expanding array of microsporidia pathogens, infecting numerous organ and tissue systems, has been detected in aquatic invertebrates. Microsporidia undergo development within the cytoplasm and, rarely, within the nucleus of host cells. Within aquatic invertebrates at least, this intracellular habit is fundamental in the ability of these pathogens to evade recognition by the host immune system. Identification of muscle-infecting microsporidia of aquatic arthropods has also played an important role in the development of a taxonomic framework for the phylum.