Wild cherry (Prunus avium L.), a partially asexual self-incompatible forest tree, shows heterozygote excess, which is a poorly studied phenomenon. In three natural populations, we found significant heterozygote excess at almost all investigated loci (eight microsatellites and markers for the self-incompatibility locus). We examined four hypotheses to account for this observed heterozygote excess. First, negative FIS can result from a lack of selfed progeny in small populations of outcrossing species. A second explanation for negative FIS is selection during the life cycle of the most heterozygous individuals. A third explanation is negative assortative mating when reproduction occurs between individuals bearing phenotypes more dissimilar than by chance. The last explanation for negative FIS relies on asexual reproduction. Expectations for each hypothesis were tested using empirical data. Patterns of FIS differed among loci. Nevertheless, our experimental results did not confirm the small sample size hypothesis. Although one locus is probably under a hitch-hiking effect from the SI locus, we rejected the effect of the self-incompatibility locus for the genome as a whole. Similarly, although one locus showed a clear pattern consistent with the selection of heterozygous individuals, the heterosis effect over the whole genome was rejected. Finally, our results revealed that clonality probably explains significant negative FIS in wild cherry populations when considering all individuals. More theoretical effort is needed to develop expectations and hypotheses, and test them in the case of species combining self-incompatibility and partially asexual reproduction.