Substantial variation was found among single‐spore cultures established from a single population of the arbuscular mycorrhizal fungus Scutellospora pellucida. A common environment experiment demonstrated that five single‐spore cultures differed in their average spore shape (as measured by length:width ratios) and size (volume) with interisolate heritabilities of offspring mean values of 0.96 and 0.87, respectively (0.66 and 0.43 for the shape and size of individual spores). The distribution of offspring spore shapes also differed in levels of variance, skewness, and kurtosis. In fact, these aspects of the distributions shifted with mean spore shape as predicted by the binomial distribution—the distribution expected due to the segregation of genetically diverse nuclei through dividing hyphae. Thus, the original parental spores generating these cultures appear to have contained genetically variable nuclei, which then segregate into the offspring spores to generate consistent differences in the mean, variance, skewness, and kurtosis of the distribution of offspring spore shapes. This nuclear segregation may be followed by the assemblage of novel combinations of nuclei through hyphal fusion. Together these processes are rarely considered mechanisms for the creation of novel genetic combinations and may contribute to the maintenance of the high level of heritable variation observed in this study.