Oceanic islands provide many opportunities for examining modes of speciation in endemic plants, especially using modern molecular methods. Most speciation has been by either cladogenesis, usually resulting in radiated complexes, or anagenesis, yielding single transformed species. Previous genetic studies with available molecular markers, representing a limited sampling of the genome, have suggested that during cladogenesis, species accrue small genetic differences but differ dramatically in morphology. An appropriate archipelago in which to evaluate the genetic consequences of cladogenesis is the Juan Fernández Islands, a national park of Chile. This present study focuses on AFLP and SSR genetic differences among and within populations of six endemic species of Erigeron (Asteraceae), restricted principally to the younger island, Alejandro Selkirk (one to two million years old). Results show that three different genetic lineages exist among these species: (1) E. rupicola and E. stuessyi; (2) E. fernandezianus; and (3) the E. ingae complex (including E. ingae, E. luteoviridis, and E. turricola). The three genetic lines are distinct from each other, and each harbors considerable genetic variation. The three species of the E. ingae complex appear to be segregating genetically but are not yet ecologically divergent. The amount of genetic differentiation among species of Erigeron is less than that already documented among species of Robinsonia (Asteraceae) on the older island (four million years old). Erigeron fernandezianus, occurring on both islands, appears to have originated on Alejandro Selkirk Island and subsequently dispersed and established also on Robinson Crusoe Island.