We analysed the phylogenetic relationships of ten of the 13 known species of the genus Apomys using DNA sequences from cytochrome b. Apomys, endemic to oceanic portions of the Philippine archipelago, diversified during the Pliocene as these oceanic islands arose de novo. Several of the speciation events probably took place on Luzon or Mindanao, the two largest, oldest, and most topographically complex islands. Only one speciation event is associated with vicariance due to Pleistocene sea-level fluctuation, and a Pleistocene diversification model in which isolation is driven by sea-level changes is inconsistent with the data. Tectonic vicariance is nearly absent from the Philippines, in which tectonic coalescence plays a significant role. Most speciation events (about two-thirds) are associated with dispersal to newly developed oceanic islands. The data imply that the species have persisted for long periods, measured in millions of years after their origins; further implications therefore are that faunal turnover is very slow, and persistence over geological time spans is more prominent than repeated colonization and extinction. Neither the equilibrium nor the vicariance model of biogeography adequately encompasses these results; a model incorporating colonization, extinction, and speciation is necessary and must incorporate long-term persistence to accommodate our observations. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80, 699–715.