Understanding the reproductive biology and breeding system of rare species is crucial for effective conservation. We examined floral biology, assessed the true pollinators, and investigated the reproductive effect of six pollination treatments (spontaneous and induced autogamy, geitonogamy, spontaneous and supplemental cross-pollination, control - flowers exposed to natural pollinators) on the fruit and seed set and their quality (size, viability) in two populations (artificial and natural) of clonal Scopolia carniolica (Solanaceae), a rare species distributed across Central and South-Eastern Europe. Hermaphroditic flowers of S. carniolica represent movement herkogamy and incomplete protogyny. Pollinators are necessary for transferring pollen onto stigmas (there was no fruit and seed set after a test for spontaneous self-pollination), and the species shows the system of obligatorily xenogamy (only cross-pollination guarantees the production of seeds with fertile embryos ensuring viable offspring) and self-incompatibility (no seeds are produced after within-flower self-pollination). Although fruits can be developed through geitonogamous self-pollination, this is associated with late-acting self-incompatibility because the seeds produced are non-viable (contain no embryos and endosperm). Bumble bees are the most effective pollinators; honeybees also contribute to pollen deposition. Conserving pollinator diversity is essential for rare clonal S. carniolica, sustaining reproduction, preventing inbreeding depression, and supporting long-term population viability.