The molecular karyotype of Paranosema grylli Sokolova, Seleznev, Dolgikh et Issi, 1994, a monomorphic diplokaryotic microsporidium, comprises numerous bright and faint bands of nonstoichiometric staining intensity. Restriction analysis of chromosomal DNAs by "karyotype and restriction display" 2-D PFGE has demonstrated that the complexity of molecular karyotype of P. grylli is related to the pronounced length polymorphism of homologous chromosomes. The background of this phenomenon is discussed in the context of ploidy state, reproductive strategy and population structure in this microsporidium. We propose that the remarkable size variation between homologous chromosomes in P. grylli may be a consequence of ectopic recombination at the chromosome extremities.