The microsporidium Nosema sp. SE is a pathogen that infects the beet armyworm Spodoptera exigua. The complete sequence of its 4,302-base pair (bp) ribosomal ribonucleic acid (rRNA) gene region was obtained by polymerase chain reaction amplification and sequencing. The rRNA organization of Nosema sp. SE was 5′-large subunit (LSU) rRNA-internal transcribed spacer-small subunit (SSU) rRNA-intergenic spacer-5S-3′, which corresponded to the pattern of Nosema bombycis. Phylogenetic analysis based on LSU rRNA and SSU rRNA both indicated that the parasite had a close relationship with other true Nosema species, confirming that Nosema sp. SE belongs to true Nosema group of the genus Nosema.