Taxonomic resolution of the Nosema/Vairimorpah clade has been augmented with DNA sequences of the small subunit (SSU) and large subunit (LSU) ribosomal RNA (rRNA) and the arrangement of SSU and LSU. Based on the two characteristics, the clade is largely divided into two, i.e. 'true' Nosema sub-group and 'non-true' Nosema sub-group within the clade. Our study shows that a novel Nosema species isolated from Pieris rapae has mixed characteristics of the 'true' and non 'true' Nosema sub-group based on the topology of SSU and LSU sequences, and rRNA of the isolate is normally organized. Additionally, the length of ITS can be a diagnostic tool to distinguish 'true' Nosema from non 'true' Nosema in the Nosema/Vairimorpha clade based on its nucleotide length as reported before. To our knowledge, this is the first report of recombination event in the Nosema/Vairimorpha clade.