Adaptive radiation is a common mode of speciation among plants endemic to oceanic islands. This pattern is one of cladogenesis, or splitting of the founder population, into diverse lineages in divergent habitats. In contrast, endemic species have also evolved primarily by simple transformations from progenitors in source regions. This is anagenesis, whereby the founding population changes genetically and morphologically over time primarily through mutation and recombination. Gene flow among populations is maintained in a homogeneous environment with no splitting events. Genetic consequences of these modes of speciation have been examined in the Juan Fernández Archipelago, which contains two principal islands of differing geological ages. This article summarizes population genetic results (nearly 4000 analyses) from examination of 15 endemic species, involving 1716 and 1870 individuals in 162 and 163 populations (with amplified fragment length polymorphisms and simple sequence repeats, respectively) in the following genera: Drimys (Winteraceae), Myrceugenia (Myrtaceae), Rhaphithamnus (Verbenaceae), Robinsonia (Asteraceae, Senecioneae) and Erigeron (Asteraceae, Astereae). The results indicate that species originating anagenetically show high levels of genetic variation within the island population and no geographic genetic partitioning. This contrasts with cladogenetic species that show less genetic diversity within and among populations. Species that have been derived anagenetically on the younger island (1–2 Ma) contain less genetic variation than those that have anagenetically speciated on the older island (4 Ma). Genetic distinctness among cladogenetically derived species on the older island is greater than among similarly derived species on the younger island. An important point is that the total genetic variation within each genus analysed is comparable, regardless of whether adaptive divergence occurs.