Technical Abstract: Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but with a size range of 2.3 Mb to 19.5 Mb the nature of the larger genomes remains unknown. Here we have undertaken genome sequence surveys of two diverse microsporidia, Brachiola algerae and Edhazardia aedis. In both we find very large intergenic regions, an abundance of transposable elements, a low gene-density and no recognizable genes that are not also found in smaller genomes. Our results demonstrate that microsporidian genome architecture varies greatly between microsporidia with varying genome size. Much of the genome size difference can be accounted for by non-coding material, such as intergenic spaces and retrotransposons, and this suggests that the forces dictating genome size may vary across the phylum. Our data suggests that either compaction or decompaction has occurred more than once within the phylum.