Microsporidia are a large group of obligate intracellular eukaryotic parasites related to fungi primarily known as parasites of vertebrates and invertebrates. They are well described as parasites of organisms of interest (e.g., edible fish and crustaceans, honeybees, bioindicators such as daphnia, humans) on which they can have an important impact (e.g., reduced survival or fecundity and sex ratio distortion). However, their diversity in aquatic environments, especially in marine ecosystems, has been greatly understudied since they are not targeted by classical eukaryotic primers used in metabarcoding studies. Moreover, little is known about their hosts among protists or microzooplankton and therefore about their impact on the trophic food web function- ing. In this work, we sampled 15 different sites across marine and freshwater environments, size-fractioned the samples, and used microsporidian specific primers associated with metabarcoding to study the microsporidian diversity (and the associated spatial variation). Co-occurrence networks as well as tyramide signal amplification- fluorescent in situ hybridization were used to link potential hosts (planktonic eukaryotes < 150 μm) and Micro- sporidia diversity. Our analysis unraveled a large microsporidian diversity which was widely divergent between the two environments studied. In both of them, an important part of this diversity was not affiliated to a genus, suggesting an important reservoir of new microsporidian species and thus new hosts among planktonic eukary- otes. Co-occurrence networks and fluorescence microscopy showed for the first-time associations between Microsporidia and dinoflagellates in freshwater and marine environments.