Microsporida are potentially useful as biological control agents for insects of economic and medical importance. Prior to their responsible use, however, an accurate and reliable means of identification to the species and subspecies level is required. Current methods used for identification are not adequate, due to variability of identifiable characters and to the occurrence of dimorphism. Recently, progress has been made in the use of biochemical characteristics to support the more traditional methods of distinguishing between morphologically similar species. We report on an improved method of characterization of microsporidan spore proteins, using 2-dimensional polyacrylamide gel electrophoresis (2D-PAGE). This method increased the number of spore polypeptides resolved from Nosema locustae spore protein extracts 2-3-fold over 1-dimensional PAGE. Also, each of the 2D-PAGE spore protein fingerprints of the species examined, namely Nosema locustae, Nosema bombycis, and Vairimorpha necatrix, were unique and differences in their spore protein composition were easily determined. The major structural proteins of Nosema locustae spores co-electrophoresed with alpha and beta tubulin from calf brain and had similar pI and molecular weight values as reported for tubulin in other species. Each species' 2D-PAGE fingerprint contained a few polypeptides that were present in relatively high concentration and these polypeptides may represent the major proteins of the structural components of the spore.