This study examined the morphological and molecular characteristics of the microsporidium Endoreticulatus sp. Zhenjiang, isolated from the silkworm (Bombyx mori). The fresh spores were oval, 2.9 ± 0.2 μm in length and 1.2 ± 0.2 μm in width. The complete rRNA cistron has a length of 4,432 bp (GenBank accession no. FJ772431), including the large subunit rRNA (2,460 bp), the internal transcribed spacer (187 bp), the small subunit rRNA (1,254 bp), the intergenic spacer (276 bp), and the 5S region (115 bp). The organization of the rRNA gene is 5'-LSU-ITS-SSU-IGS-5S-3', which is reverse compared to the organization of most microsporidian rRNA regions. Phylogenetic analysis based on small subunit rRNA sequences showed that this isolate belongs to the genus Endoreticulatus, and is closely related to Glugoides intestinalis. Furthermore, both had a similar reverse arrangement of the rRNA gene. Our study provides another example of a microsporidian species with a novel organization of rRNA genes, demonstrating that the reverse arrangement is exhibited not only by the microsporidian genus Nosema but may also occur in a clade that contains the genera Endoreticulatus and Glugoides.