ABSTRACT: The microsporidian Nosema antheraeae is a pathogen of the Chinese oak silkmoth Antheraea pernyi, the molecular karyotype of which is still poorly understood. Here the diplokaryon of N. antheraeae strain NP‐YY has been visualized both by fluorescence and electron microscopy. In addition, pulsed‐field gel electrophoresis (PFGE) showed that the haploid genome of N. antheraeae is approximately 9.3–9.5 million base pairs organized into 15 chromosomal bands. The mean fluorescence intensity of N. antheraeae and Nosema bombycis DNA measured by flow cytometry confirmed that the genome size of these two species was congruent with measurements obtained by PFGE. These initial results on the chromosome organization of N. antheraeae provide a foundation for the comparative genomics of N. antheraeae with other species of Nosema.