The California Channel Islands are a group of eight oceanic islands located off the coast of southern California that are substantially closer to the mainland than most other well-studied island systems. The equilibrium theory of island biogeography proposed by MacArthur and Wilson posits that species diversity on an island will be positively impacted by island area and negatively impacted by isolation, which has been confirmed for the Channel Islands. In this study, we have extended MacArthur and Wilson's theory to examine how levels of genetic diversity relate to four island characteristics (island area, distance to the mainland, distance to the nearest island, plant diversity) in the endemic perennial taxa of Acmispon (Fabaceae) on the Channel Islands. We sampled two island species of Acmispon, A. argophyllus and A. dendroideus, from all islands, and mainland sister taxa for nuclear microsatellites, low-copy nuclear sequence and plastid sequence data. We found that only one measure of diversity from one genetic region (low-copy nuclear) was correlated with island area, that there was no support for a relationship between genetic diversity and distance to the mainland and that distance to the nearest island was a predictor of low-copy nuclear genetic diversity. Plant diversity was a significant predictor of plastid genetic diversity when considering all samples. We conclude that the equilibrium theory of island biogeography does not hold for measures of genetic diversity in the Channel Island endemic Acmispon based on island area and distance to the mainland. The short distance between individual islands and the mainland probably facilitates a moderate rate of mainland to island dispersal, preventing the islands from functioning as isolated biogeographic units. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 289–304.