We investigated whether the plants of the Galápagos Archipelago and Cocos Island, which are each other's closest neighboring insular systems, show any such sister relationships. Five genera of vascular plants have endemics in both archipelagos, including plants with different life histories and dispersal mechanisms: tree ferns, epiphytes, trees, herbs, and shrubs, with adaptations for dispersal by wind or birds (two genera each) or with no obvious dispersal adaptation (one genus). We obtained molecular phylogenies for these genera to test the hypothesis of phytogeographical links between the islands. The phylogenies for all five genera were not consistent with this hypothesis, but they supported floristic studies in revealing no direct phytogeographical links between the islands. We attribute this lack of floristic affinity primarily to air and ocean circulation patterns that limit dispersal between Galá pagos and Cocos and to a low frequency of interisland bird movements. There are also major ecological differences between them, and Cocos Island is quite small, which limits the chance of random dispersal events and subsequent establishment.