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Assuming that a male's genetic characteristics affect those of his offspring, extra-pair copulation has been hypothesized to increase heterozygosity of the progeny—the “genetic compatibility” hypothesis—and the genetic diversity within litters—the “genetic diversity” hypothesis. We tested these two hypotheses in the alpine marmot (Marmota marmota), a socially monogamous mammal showing a high rate of extra-pair paternity (EPP). In a first step, we tested the assumption that a male's genetic characteristics (heterozygosity and genetic similarity to the female) affect those of his offspring. Genetic similarity between parents influenced offspring heterozygosity, offspring genetic similarity to their mother, and litter genetic diversity. The father's heterozygosity also influenced litter genetic diversity but did not affect offspring heterozygosity. Hence, heterozygosity seems not to be heritable in the alpine marmot. In a second step, we compared genetic characteristics of extra-pair young (EPY) and within-pair young (WPY). EPY were less genetically similar to their mother but not more heterozygous than WPY. EPY siblings were also less genetically similar than their WPY half siblings. Finally, the presence of EPY promoted genetic diversity within the litter. Thus, our data support both the “genetic compatibility” and the “genetic diversity” hypotheses. We discuss further investigations needed to determine the primary causes of EPP in this species.