Abstract: We did a comparative analysis of the small subunit ribosomal DNA (rDNA) for two species of Microsporidia, Semenovaia chironomi and Neoperezia chironomi, both parasites of Chironomus plumosus (Diptera, Chironomidae). These two microsporidial species have been described previously on the basis of light and electron microscopic studies. The former species is dimorphic, producing both single diplokaryotic spores and uninucleate spores in sporophorous vesicles (SPVs) in packets of 16, while the latter species is monomorphic, disporoblastic, producing only uninucleate spores in SPVs. Based on their life cycles, S. chironomi and N. chironomi were assigned to two different families, Burenellidae and Neopereziidae. However, molecular analysis shows 96.7% sequence similarity for the small subunit rDNA between these two species. Remarkable similarities of the spore ultrastructure (mainly of the extrusion apparatus) justify a transfer of S. chironomi to Neoperezia, establishing a new combination, Neoperezia semenovaiae. Neoperezia belongs to Clade V, Class Aquasporidia sensu , and is in its spore ultrastructure similar to its closest relatives, namely Bryonosema, Schroedera, Pseudonosema, Trichonosema and Janacekia. We therefore conclude that similarities in spore ultrastructure reflect the phylogenetic relatedness of these Microsporidia, as opposed to the strikingly diverse life cycles. [Copyright &y& Elsevier]