Twenty-three flavonoids were isolated from the leaves of two species of Sophora (Fabaceae) from the Juan Fernandez Islands (S.. fernandeziana and S. masafuerana), two related species from continental Chile (S. macrocarpa and S. microphylla) and one sample from New Zeland (S. microphylla). A phenetic analysis was used to evaluate chemical similarities. Flavonoid profiles suggest that Chilean and New Zealand populations of S. microphylla are most closely related to each other. Sophora masafuerana appears most closely related to S. microphylla and this pair of species is also fairly closely related to S. fernandeziana. S. macrocarpa is more distantly related to the cluster of other species. The results suggest that the two Juan Fernandez endemic species are derived from two separate introductions. The exact origin of S. masafuerana remains unclear, as the evidence does not enable us to distinguish between or clarify its possible relationships with New Zealand or South American populations.