We addressed the evolutionary relationships and biogeographical patterns of a model organism of low relative dispersal ability by electrophoretically assaying the products of 42 presumptive gene loci in Philippine and Bornean members of the Rana signata complex of SE Asian stream frogs. Utilizing three distantly related species of ranid frogs to deeply root trees consisting of five more closely-related species and six in-group species of the Rana signata complex, we conducted phylogenetic analyses that produced concordant topologies, regardless of the data coding strategy employed. All analyses support the hypothesis of monophyly for the Rana signata complex on the whole, but none provides support for the monophyly of its Philippine members. Our analyses of morphometric and allozyme data (along with biogeographical information) indicate that (1) most previously-recognized Philippine and Bornean subspecies of the Rana signata complex should be recognized as full species in appreciation of their status as independent evolutionary lineages; (2) Rana picturata Boulenger (until very recently included in the synonymy of Rana signata signata) is deserving of specific rank; (3) the Mindoro Isl. (Philippine) population, previously confused with Rana signata similis of Luzon Isl. is a new species; (4) two major clades (((R. signata (R. grandocula + R. similis)) + (R. picturata (R. mangyanum + R. moellendorffi))) of Bornean + Philippine lineages are recognized, corresponding to two separate faunal exchanges between the Philippines and the edge of the Sunda Shelf; (5) invasions of the oceanic portions of the Philippine islands from the Sunda Shelf have occurred along both the eastern (Sulus–Mindanao–Samar–Leyte–Luzon) arc and the western (Palawan–Busuanga–Mindoro) island arcs; (6) northern reaches of Wallace’s Line (as modified by Huxley) include exceptions to an otherwise discrete faunal separation. These results suggest the need for revision of this biogeographical barrier, increased recognition of temporal patterns of island connectedness and geographical proximity, and/or a greater appreciation of dispersal abilities of ranid frogs. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 76, 393–461.