Microsporidian isolates from five lepidopteran pests-Spodoptera litura, Spodoptera exigua, Helicoverpa armigera, Plutella xylostella, and Pieris spp.-were compared by spore morphology, infectivity to S. litura, Western-blot banding patterns, the sequences of small subunit rRNA gene (SSUrRNA sequence), and random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR). All the isolates could infect experimentally and multiply in the larvae of S. litura. The S. exigua isolate showed the highest virulence to the larvae of S. litura while the P. xylostella isolate showed the lowest. No significant differences either in spore morphology or in SSUrRNA sequences of these isolates were found. The SSUrRNA sequences of these isolates confirmed they are members of the genus Nosema. Based on the result of Western-blot hybridization with the rabbit anti-Nosema spodopterae spore antiserum, three serotypes could be distinguished: N. spodopterae (S. litura isolate) and Pi. spp. isolate; S. exigua and H. armigera isolates; and P. xylostella isolate. The amplicons of RAPD-PCR with 60 primers yielded clear patterns that were selected and used for identification and also for phylogenic analysis of these five isolates. Based on analysis by the computer, isolates could be clearly divided into three groups that were coincident with the serotypes; therefore we suggest that N. spodopterae and isolates of Pi. spp., S. exigua, and H. armigera are more closely related in phylogenesis. In addition, in the amplification with the Nosema bombycis specific primer set, only DNAs from P. xylostella isolate and N. bombycis yielded amplicons. Therefore, we suggest that four isolates, excluding the P. xylostella isolate, are N. spodopterae, and the taxonomic position of P. xylostella isolate needs to be elucidated.