The exact order of divergence in deep regions of the eukaryotic tree is controversial. On the lineage that leads to the Fungi there are thought to be two other groups; the first to diverge are the nucleariid amoebae, and the next the Microsporidia. Microsporidia are either the sister group to the Fungi, or lie within the Fungi (Figure 1), and they should be included in studies of fungi. They are unculturable, obligate parasites of animals, including humans. They have extremely reduced eukaryotic genomes — with a genome size of ∼2.6 Mb and ∼2000 genes [9] — remnant mitochondria, and unique morphologies related to parasitism, including a very frightening polar tube used to initiate infection [9].