The study reports the genome sequence of *Encephalitozoon cuniculi*, a microsporidian parasite with a highly reduced genome of approximately 2.9 megabases (Mb). The genome contains 11 linear chromosomes, each ranging from 217 to 315 kb in size. The genome is characterized by compacted structure, with reduced intergenic spacers and short proteins compared to their eukaryotic orthologues. The strong host dependence of *E. cuniculi* is evident from the absence of genes for certain biosynthetic pathways and the tricarboxylic acid cycle. Phylogenetic analysis supports the fungal affiliation of microsporidia. Notably, the genome contains genes related to mitochondrial functions, suggesting the retention of a mitochondrion-derived organelle, possibly a mitosome. The mitosome hypothesis is supported by the presence of genes involved in Fe-S cluster assembly and other mitochondrial functions. The study also highlights the simplified metabolic capacities and transport systems in *E. cuniculi*, including the lack of genes for fatty acid β-oxidation, respiratory electron transport, and the tricarboxylic acid cycle. The findings provide insights into the metabolism, general biology, and evolutionary history of microsporidia, as well as the potential role of the mitosome in their survival and adaptation to parasitic lifestyles.The study reports the genome sequence of *Encephalitozoon cuniculi*, a microsporidian parasite with a highly reduced genome of approximately 2.9 megabases (Mb). The genome contains 11 linear chromosomes, each ranging from 217 to 315 kb in size. The genome is characterized by compacted structure, with reduced intergenic spacers and short proteins compared to their eukaryotic orthologues. The strong host dependence of *E. cuniculi* is evident from the absence of genes for certain biosynthetic pathways and the tricarboxylic acid cycle. Phylogenetic analysis supports the fungal affiliation of microsporidia. Notably, the genome contains genes related to mitochondrial functions, suggesting the retention of a mitochondrion-derived organelle, possibly a mitosome. The mitosome hypothesis is supported by the presence of genes involved in Fe-S cluster assembly and other mitochondrial functions. The study also highlights the simplified metabolic capacities and transport systems in *E. cuniculi*, including the lack of genes for fatty acid β-oxidation, respiratory electron transport, and the tricarboxylic acid cycle. The findings provide insights into the metabolism, general biology, and evolutionary history of microsporidia, as well as the potential role of the mitosome in their survival and adaptation to parasitic lifestyles.