The knowledge on life cycles and biology of the Microsporidia and the Myxozoa is summarised. These two groups are placed together due to their similarities (intracellular development, spore stages for transmission, ejectable polar “filament”) and the historical fact that they were assigned to the common taxon “Cnidospora” prior to being correctly classified. We would like to emphasise here that these groups are taxonomically far apart. While the Microsporidia are related to the fungi, the Myxozoa belong to the Cnidaria and are therefore metazoans. Both are important parasites of aquatic organisms. Microsporidians can infect a wide range of hosts from protists to vertebrates. They can be directly (horizontally) transmitted via spores or vertically via the gonads to the offspring. Life cycles can be simple (monoxenous, one host species) or complex (heteroxenous, multi-host life cycles), some including phases of both horizontal and vertical transmission. Myxozoans, on the other hand, require two obligate hosts in their life cycle, a vertebrate intermediate and an invertebrate final host. Transmission to the vertebrate host is mediated by free-floating actinospores, while the invertebrate host becomes infected by myxospores that are mostly in sediments. Both groups contain species of economic relevance and ecological impact.