A microsporidium was isolated from larvae of Spodoptera litura (Fabricius) collected from Tamil Nadu, India. This microsporidian species is monomorphic, disporous and develops in direct contact with the cytoplasm of the host cell. The nuclear configuration of merogonic and sporogonic stages was diplokaryotic. The merogonic proliferative stage was unusual that normal development with 1, 2 and 4 binucleated forms were common, while large multinucleate meronts containing 8 and 12 small compact horseshoe-like diplokaryotic nuclei were also observed. The fresh spores were typically ovocylindrical in shape, with a mean size of 3·91×1·91 μm and the polar filament length was ~90 μm. Infection was systemic with mature spores produced in the midgut, nervous tissue, muscles, labial glands, gonads, tracheae, epidermis, Malpighian tubules and, most extensively, fat body tissues. The new isolate was highly pathogenic to S. litura larvae. Host specificity tests performed on 37 non-target hosts of 5 different insect orders revealed that the new isolate is pathogenic only to lepidopteran insects. We sequenced the 16S small subunit rRNA (SSU rRNA) gene of the isolate and compared it with 72 non-redundant microsporidian sequences from the GenBank. Based on the light microscopic studies and phylogenetic analyses, the new isolate is assigned to the genus Nosema. Significant differences in the SSU rRNA sequence were identified when compared with the type species Nosema bombycis and other closely related species viz., Nosema spodopterae. Structural differences were also observed in the 16S SSU rRNA between the new isolate and the two above-mentioned microsporidian pathogens. We conclude that the microsporidian isolate reported here is distinctly different from the other known species and is likely to be a new species.