Arbuscular mycorrhizal fungi (Glomeromycota) are the dominant symbionts of land plants and one of the oldest multicellular lineages that exist without evidence of sexual reproduction. The mechanisms that protect these organisms from extinction due to accumulation of deleterious mutations in the absence of sexual recombination are unclear. Glomeromycota reproduce by spores containing hundreds of nuclei, which represents a departure from the typical eukaryotic developmental pattern, where a multicellular organism is re‐created from a uninucleate propagule. To understand whether the multinucleate spore makeup may have contributed to the evolutionary success of Glomeromycota, we examined the dynamics of spore nuclei in Glomus etunicatum using live three‐dimensional imaging and mathematical models. We show that the spores are populated by an influx of a stream of nuclei from the surrounding mycelium rather than by divisions of a single founder nucleus. We present evidence that mechanisms of selection are likely to operate at the level of individual nuclei. On the basis of mathematical analyses of the effects that these nuclear dynamics have on the population mutation load, we postulate that the developmental patterns of sporogenesis have adaptive significance for moderating the accumulation of deleterious mutations and may have contributed to the evolutionary longevity of Glomeromycota.