Microsporidia are ubiquitous obligate intracellular parasites of all major animal lineages. They are important pathogens of mammals and invertebrates, and are now one of the most common infections amongst immuno-compromised humans. Microsporidia are unusual eukaryotes with very small genomes (as small as 2.3 MB), highly reduced biochemical pathways and pared down mitochondria called mitosomes.