The genus Scalesia is endemic to the Galápagos Islands. Scalesia cordata is a tree occurring only in the southern part of Isabela as small, remnant populations of larger forests. We studied the reproductive ecology of a population protected in an enclosure in order to reveal the extent to which the reproductive system limits the recruitment of young individuals. Pollinator observations revealed that each capitulum received, on average, 2.5 visits per hour and exposed receptive stigmas received many pollen grains. Even so, the seed set and recruitment of trees was poor. Crossing experiments showed that S. cordata produced about twice as many fertile seeds after outcrossing than after selfing. In addition, self-pollinated capitula flowered for a longer time than outcrossed capitula (3.8 ± 1.1 days vs. 2.1 ± 0.8 days). These results may suggest that the species is partly self-incompatible, as other species of the genus. The small population size, with its potential derived consequences, is most certainly a prominent threat to S. cordata. The pressure from introduced plant species found in the enclosure also contributes to the seemingly poor condition of the population. To recover S. cordata, we suggest enlarging the enclosure, removing the introduced plant species and continuing to cultivate plants as a genetic reserve. Introducing new genetic material is likely to increase the seed set of the population