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Heterokaryosis (from the Greek heteros, meaning other and karyon, meaning kernel) is a term used in mycology meaning to have two or more genetically different nuclei within the same mycelium of a fungus.

Many fungi (notably the arbuscular mycorrhizal fungi) exhibit this phenomenon. The nuclei within the same mycelium may differ from one another either through the accumulation of mutations or through the fusion of genetically distinct fungal hyphae. This can lead to individuals that have different nuclei in different parts of their mycelium. In this case, the notion of individual itself becomes vague since the rule of one genome = one individual does not apply any more.