Cabbage butterfly (Pieris rapae), included in the Lepidoptera genus, Pieris family, is the main pest that damages Cruciferae. In this paper, we reported a microsporidian isolate of Nosema species which was isolated from P. rapae in Zhenjiang City, Jiangsu Province, China. The mature spore of this microsporidium is long oval in shape and 3.8 ± 0.3 × 2.0 ± 0.2 μm in size. Research results showed that the novel microsporidium cannot infect the BmN cell in vitro and silkworm larvae. The organization of rRNA gene was 5'-SSU rRNA-ITS-LSU rRNA-3'. Phylogenetic trees based on SSU rRNA and LSU rRNA gene sequences were constructed by MEGA 4.0 software. The topology showed that this microsporidium was on the same second branch of Nosema clade, and had close relationships to other Nosema species. Consequently, this microsporidium was confirmed to be a member of Nosema genus, and named as Nosema sp. MPr.