Microsporidia Nosema bombycis is a fungal pathogen that causes epidemic pebrine disease in Bombyx mori. Two N. bombycis isolates were obtained from two areas in China and showed different pathogenicity after Spodoptera frugiperda Sf9 cell cultivation. The regions of rDNAs from different isolates were analyzed, suggesting no relationship between the genetic divergence and their geographic distributions. Further analysis showed that several copies of SSU rDNA units in N. bombycis were interrupted by a MITE-like transposon, indicating the complexity of genomic structure in Nosema bombycis.