Reproductive and pollination biology studies are crucial to understand processes of diversification in plants. The facultative apomictic orchid Zygopetalum mackayi comprises a potential model in the Neotropics to understand the role of asexuality in the reproductive success of plants. Adventive embryogenesis is the main mechanism behind the production of clonal embryos in Z. mackayi and it has been associated with polyembryony. Previous studies suggested all seeds (mono-/polyembryonic) to be of apomictic origin. If so, we expect to find no difference in seed viability from self- and cross-pollinations, considering monoembryonic and polyembryonic seeds. To test this prediction, we estimated how pollen origin affects fruit set and seed viability. We also investigated if reproduction is dependent on pollinators and described how pollination is achieved. We collected phenological and pollination data in one natural population and sampled five additional populations for studies of the reproductive system. To access seed viability, we stained seeds with a tetrazolium solution. Z. mackayi is a generalized food-deceptive species pollinated by Bombus pauloensis. This species is also dependent on pollinators for reproduction as individuals are unable to perform spontaneous self-pollination. Self- and cross-pollination treatments yielded mainly monoembryonic seeds, but crossed flowers produced more viable monoembryonic seeds than self-pollinated ones. Sexual reproduction is dominant in Z. mackayi because monoembryonic seeds are more frequent in both cross- and self-pollinated flowers and more viable when pollen comes from a different individual. Self-pollinated flowers set more polyembryonic seeds than crossed ones, although there were no differences in seed viability between treatments considering all types of seeds produced. We hypothesize that embryo abortion by inbreeding depression in self-pollinated flowers is compensated by apomictic reproduction in Z. mackayi, as polyembryonic seeds are a common outcome of apomixis. We propose polyploidy, not pollen limitation, is responsible for the evolution of apomixis in this orchid species.