The nature of variation in morphological characters in spores of arbuscular endomycorrhizal fungi (Order Glomales, Class Zygomycetes) has received little attention, despite the importance of these characters in modern taxonomy of the order. We tested the hypothesis that genetic variation exists in spore size and color (presumably important taxonomic characters) within a single isolate of the glomalean fungus Glomus clarum. Phenotypic variation in size and color of spores was determined from a pot culture population (designated P). A 10% selection pressure was imposed on replicate pot cultures of the first progeny culture generation (G1) by selecting the smallest, largest, yellowest, and whitest spores from the P generation and inoculating Sorghum bicolor plants. The experiment was repeated for another generation (G2), but with a 5% selection pressure. In both the G1 and G2 generations, significant differences in spore size and color were observed among the various treatments, indicating substantial genetic variation in these characters. Despite efforts to keep the physical environment constant across generations, we observed variation in the overall means of spore size and color among the generations (regardless of treatment), indicating a strong nongenetic influence on character expression. This study provides empirical evidence that will help delimit species boundaries among isolates of Glomus clarum and similar morphospecies. It also demonstrates a promising method to help elucidate the nature of character diversity in obligately asexual fungi.