We sequenced 15 complete mitochondrial genomes and performed comprehensive molecular phylogenetic analyses to study the origin and phylogeny of the Hynobiidae, an ancient lineage of living salamanders. Our phylogenetic analyses show that the Hynobiidae is a clade with well resolved relationships, and our results contrast with a morphology-based phylogenetic hypothesis. These salamanders have low vagility and are limited in their distribution primarily by deserts, mountains, and oceans. Our analysis suggests that the relationships among living hynobiids have been shaped primarily by geography. We show that four-toed species assigned to Batrachuperus do not form a monophyletic group, and those that occur in Afghanistan and Iran are transferred to the resurrected Paradactylodon. Convergent morphological characters in different hynobiid lineages are likely produced by similar environmental selective pressures. Clock-independent molecular dating suggests that hynobiids originated in the Middle Cretaceous [Ϸ110 million years ago (Mya)]. We propose an ''out of North China'' hypothesis for hynobiid origins and hypothesize an ancestral stream-adapted form. Given the particular distributional patterns and our molecular dating estimates, we hypothesize that: (i) the interior desertification from Mongolia to Western Asia began Ϸ50 Mya; (ii) the Tibetan plateau (at least on the eastern fringe) experienced rapid uplift Ϸ40 Mya and reached an altitude of at least 2,500 m; and (iii) the Ailao-Red River shear zone underwent the most intense orogenic movement Ϸ24 Mya.mitochondrial DNA ͉ phylogenetics ͉ homoplasy ͉ Tibetan Plateau T he Asiatic Salamanders, Hynobiidae, represent an early branch of the caudate lineage (1). All living species (Ϸ50, in seven to nine genera; http:͞͞amphibiaweb.org) occur in Asia. Hynobiids are closely related to the family Cryptobranchidae, with which they form the suborder Cryptobranchoidea. In comparison with other living salamanders, hynobiids are thought to resemble the most recent common ancestor of all salamanders because of three traits that are regarded as ancestral: external fertilization, an angular bone in the lower jaw, and large numbers of microchromosomes (1-3). Although usually thought to be monophyletic, the Hynobiidae also has been considered a paraphyletic stem group (4). Fossil hynobiids are known from the Late Miocene [Ϸ5 million years ago (Mya)] (5), whereas their relatives, cryptobranchids, can be traced back to the Jurassic (Ϸ160 Mya) (6). Remarkably, recent fossil findings of salamanders from the Early Cretaceous of North China show strong similarities with the Hynobiidae with respect to many skeletal features (7-9). This finding raises the questions of where and when hynobiids originated and what relationship there is between them and their fossil relatives. To answer these questions, a robust phylogenetic hypothesis of living hynobiids is required. Apart from a tentative phylogeny based on 23 morphological characters ( Fig. 1; ref. 10), and another based on an unpublished data...