Abstract  A previous study showed that some individuals of the tetraploid Galápagos endemic Scalesia affinis were able to produce offspring after selfing. The present study compares the fitness of self-pollinated offspring with the fitness of cross-pollinated offspring. Germination success, seedling survival, and four different growth parameters was measured. In most of the studied characters selfed offspring were significantly inferior to outcrossed progeny. The effect was very clear in germination and survival. Outcrossed embryos were 3.4 times more likely to germinate than those that were selfed-fertilized, and the mortality was 84% higher among selfed individuals. Also, there was no genetic variation in inbreeding depression. The present study is based on material from a large population on Isabela Island, Galápagos. At other localities in the archipelago, populations have been through recent dramatic bottlenecks due to the grazing of introduced mammals. Considering the significant inbreeding depression found in the large population and the presence of a partial self-incompatibility system, these small populations are likely to be highly vulnerable and their future survival critically threatened.