The Sunda region of south-east Asia comprises the Malay Peninsula and the islands of Java, Sumatra and Borneo, all of which lie on a shallow continental shelf projecting from Indochina. Pleistocene glacial cycles caused sea levels to drop repeatedly, exposing vast areas of the Sunda shelf and creating land bridges among the islands and mainland. These land bridges, the latest of which connected all three of the major Sunda islands to the Malay Peninsula as recently as 9500 years ago, may have enabled mammalian migrations across the Sunda shelf. Pleistocene land bridges on the Sunda shelf have been invoked to explain the current distributions of mammalian taxa occupying ranges corresponding with the Pleistocene limits of land and the appearance of new mammal species in the Pleistocene fossil record. The ability of mammals to move throughout the exposed shelf during periods of low sea level would, however, have been influenced by topographic and ecological features, which have been variously described as savanna-like or as moist tropical rain forest. Using a phylogeographical approach, we test the hypothesis that Pleistocene land bridges enabled widespread movements in three rain-forest-restricted murine rodents of the Sunda shelf: Maxomys surifer, Leopoldamys sabanus and Maxomys whiteheadi. Our results do not support the hypothesis of broad Pleistocene migrations in these taxa, but instead suggest a deep history of vicariant evolution that may correspond with the Pliocene fragmentation of the Sunda block. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 91–109.