<jats:p>• <jats:italic>Premise of the study:</jats:italic> Anagenesis (or phyletic evolution) is one mode of speciation that occurs in the evolution of plants on oceanic islands. Of two endemic species on the Juan Fernández Islands (Chile), <jats:italic>Myrceugenia fernandeziana</jats:italic> and <jats:italic>M. schulzei</jats:italic> (Myrtaceae), believed to have originated anagenetically from different continental progenitors, the first is endemic to Robinson Crusoe Island and has no clear tie to continental relatives; the last is endemic to the younger island, Alejandro Selkirk Island, and has close affinity to <jats:italic>M. colchaguensis</jats:italic> in mainland Chile.</jats:p><jats:p>• <jats:italic>Methods:</jats:italic> Using AFLPs and six nuclear microsatellites from 381 individuals representing 33 populations, we determined patterns of genetic variation within and among populations on both islands and between those of the islands and mainland.</jats:p><jats:p>• <jats:italic>Key results:</jats:italic> Considerable genetic variation was found within populations on both islands. The level of gene diversity within <jats:italic>M. schulzei</jats:italic> was equivalent to that of its close continental relative <jats:italic>M. colchaguensis</jats:italic>. Genetic diversity was not partitioned geographically in <jats:italic>M. fernandeziana</jats:italic> and was weakly so and nonsignificantly in <jats:italic>M. schulzei</jats:italic>.</jats:p><jats:p>• <jats:italic>Conclusions:</jats:italic> The high genetic variation in both taxa is most likely due to anagenetic speciation. Subsidence of the older island Robinson Crusoe, landscape erosion, and restructuring of communities have severely reduced the overall island population to a single panmictic system. On the younger and less modified Alejandro Selkirk Island, slightly stronger patterns of genetic divergence are seen in <jats:italic>M. schulzei</jats:italic>. Because both species are genetically diverse and number in the thousands of individuals, neither is presently endangered in the archipelago.</jats:p>