Sequences of the small subunit rRNA genes of Amblvospora california and an Amblyospora sp. from Culex salinarius were determined. These sequences were compared phylogenetically with 16 other microsporidia. The results suggest Amblyospora forms a sister taxon to the rest of the microsporidia examined. The basal position of Amblyospora is discussed with respect to the evolution of microsporidian life cycles. These sequences represent the longest microsporidian small subunit rRNA genes sequenced to date, 1,359 and 1,358 bp. respectively. Structural features and GC content (49% for both) are comparable to those of other microsporidia which have been sequenced.