Pollination ecology and breeding system of Lilium pomponium L. were studied, and their effect on the reproductive outcome was assessed. This species has high conservation interest in Europe, because it is included in Annex V of the EU Habitat Directive and it is one out of the five Lilium species listed in IUCN Global Red List. To achieve our aim, the pollen vectors as well as the effect of bagging, emasculation and artificial pollination on reproductive output were studied. The most frequent visitor was the Lepidopteran Gonepteryx rhamnii. In general, reproductive outputs were close to zero for all the self-pollination treatments; however, geitonogamy and facilitated selfing seem slightly more efficient than autogamy, as also confirmed by self-compatibility and autofertility indices. Altogether, our results suggest a self-incompatible outcrossing breeding system, with a poor capacity for selfing. Nevertheless, climate change and anthropic threats might promote a shift toward self-fertilization, even maladaptive, favouring the few individuals able to produce selfed seeds.