Spore ornamentation of Haplosporidium nelsoni and Haplosporidium costale was determined by scanning electron microscopy. For H. nelsoni, the spore surface was covered with individual ribbons that were tightly bound together and occurred as a single sheet. In some spores, this layer was overlaid with a network of branching fibers, about 0.05 μm in diameter, which often was dislodged from the spore at the aboral pole. For H. costale, ornamentation consisted of a sparse network of branching fibers on the spore surface. Molecular phylogenetic analysis of the phylum Haplosporidia revealed that Urosporidium, Bonamia, and Minchinia were monophyletic but that Haplosporidium was paraphyletic. All species of Minchinia have ornamentation composed of epispore cytoplasm, supporting the monophyly of this genus. The presence of spores with a hinged operculum and spore wall-derived ornamentation in Bonamia perspora confounds the distinction between Bonamia and Haplosporidium. Species with ornamentation composed of outer spore wall material and attached to the spore wall do not form a monophyletic group in the molecular phylogenetic analysis. These results suggest that the widely accepted practice of assigning all species with spore wall-derived ornamentation to Haplospordium cannot be supported and that additional genera are needed in which to place some species presently assigned to Haplosporidium.