Different pollination treatments of capitula were used to examine the breeding system of individuals of the tetraploid endemic species Scalesia affinis from the Galápagos Islands. All types of crossings resulted in approximately 35 achenes per capitulum, but in actively and passively self-pollinated capitula these were mostly without embryos. Among self-pollinated individuals a large variation was found in the production of embryos. Some individuals failed completely to set filled achenes while others produced few or many. Additionally, we found a clear difference in female phenology of florets in self-pollinated capitula compared with florets in cross-pollinated capitula. Female florets in self-pollinated capitula remained receptive for longer time. These results suggest that Scalesia affinis is partly self-incompatible. Outcrossing is assured by the endemic carpenter bee, Xylocopa darwini, which proved to be an important pollinator of Scalesia affinis. Nevertheless, geitonogamy seemed to be considerable in the focal population, for which reason open pollinated capitula produced fewer achenes than controlled outcrossed capitula.