Hexaploid seeds are produced by predominantly tetraploid populations of Hypericum perforatum, but the fate of hexaploid seedlings and their reproductive behavior have not been closely examined. We used flow cytometry to analyze single seeds and individual plant samples of three accessions of H. perforatum to determine ploidy levels and reproductive pathways. Seed samples of all three accessions were facultative apomicts, with tetraploid cytotype predominant (85–91%) and a lower frequency of hexaploids (9–14%), with diploids (5%) detected in only one population. Seedling populations consisted of tetraploids (87–97%) and hexaploids (3–13%). Hexaploid embryos are most likely generated by a 2n gamete of the tetraploid and fertilized by a normal, reduced tetraploid male gamete. These hexaploids are expected to produce unbalanced gametes because they possess chromosome complements that include two triploid sets originally derived from two different species. The observation that some tetraploid seeds had endosperm with high cellular DNA content indicates that some unbalanced male gametes produced by hexaploids were evidently viable and could effect fertilization. Whether this mechanism is also true for egg cells or whether the hexaploids are capable of producing unreduced embryo sacs is uncertain. Because of severe reproductive difficulties, hexaploid seedlings may play a very minor role in gene flow and the further evolution of H. perforatum. The likelihood that hexaploids will evolve to types with an increased frequency of bivalent paring in meiosis is relatively low. However, hexaploids may include novel chemotypes, which could be vegetatively propagated if valuable, medicinal types can be identified among them.