Myxozoans are highly diverse and globally distributed cnidarian endoparasites in freshwater and marine habitats. They have adopted a heteroxenous life cycle, including invertebrate and fish hosts, and have been associated with diseases in aquaculture and wild fish stocks. Despite their importance, genomic resources of myxozoans have proven difficult to obtain due to their miniaturized and derived genome character and close associations with fish tissues. The first ‘omic’ datasets have now become the main resource for a better understanding of host–parasite interactions, virulence, and diversity, but also the evolutionary history of myxozoans. In this review, we discuss recent genomic advances in the field and outline outstanding questions to be answered with continuous and improved efforts of generating myxozoan genomic data. The first myxozoan genome assembly was published in 2015, and myxozoan genomics has since become a rapidly progressing field, with limitations due to DNA contamination from largely polyploid fish hosts.Myxozoan genomes are amongst the smallest metazoan genomes on Earth with important gene reductions and loss of basic biological functions such as DNA methylation and, in one case, the mitochondrial genome.The evolutionary history of myxozoans appears to confirm a sister relationship of the Myxozoa and Polypodium hydriforme but their old age and derived genome characteristics obscure evolutionary analyses.The first metagenomic study using aquatic eDNA highlights the importance of using genomic approaches for uncovering the strongly underestimated myxozoan biodiversity.Comparative transcriptomics highlighted protease-encoding genes as candidate gene groups for therapeutics and vaccine design.