Knowledge of processes responsible for seed dormancy can improve our understanding of the evolutionary dynamics of reproductive systems. We examined the influence of the breeding system on primary seed dormancy in Hypericum elodes, an Atlantic–European softwater pools specialist plant that exhibits a mixed mating strategy (the ability to both self- and cross-pollinate) to set seeds. Seeds were obtained through hand pollination treatments performed in a natural population during three consecutive years. Primary dormancy of seeds recovered from each pollination treatment was measured by analysing the seed germination response at dispersal and after various periods of cold stratification. While all collected seeds exhibited physiological dormancy, the degree of primary dormancy was associated with the pollination treatments. Weak and rapid loss of primary dormancy characterized seeds recovered from self-pollinated flowers, while stronger dormancy was found in seeds obtained from cross-pollination. The association between pollination treatments and primary dormancy indicated that the mating system should be considered as a source of variation for dormancy degree, proportional to self- and cross-pollinations (selfing rate) within populations of this species. These results suggest that by shedding seeds with various degrees of dormancy, plants may distribute their offspring across time by means of polymorphism in germination response. We conclude that seed germination alone is not an appropriate fitness measure for inbreeding depression estimates, unless dormancy is removed.