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Crocodile newts (Echinotriton and Tylototriton) are emblematic of the biodiversity of South-East Asia. In this study, we provide an account of their evolution, diversity and phylogeography based on mitochondrial (16.2 kb) and nuclear sequences (3.2 kb), combining barcoding data from nearly 1200 specimens collected over ~180 localities, representative of all lineages known to date. While phylogenies of nuclear data lacked resolution, the mitochondrial tree showed dynamic allopatric speciation that followed climate cooling during the last 10 million years, a pattern shared with many other tropical and subtropical amphibians. In crocodile newts, this implies weak dispersal and local adaptation as contributing factors of isolation, and was accompanied by macro- and micro-evolutionary changes in reproductive behaviours. Specifically, our resolved phylogeny of Tylototriton allowed the tracing of a major shift from conserved habits of terrestrial clutch-spawning towards more plastic strategies involving both aquatic and land spawning of single eggs. Using this framework, we then revised the taxonomy of crocodile newts by describing a new subgenus and two new species. Our study provides a basis to guide future phylogeographic, speciation and conservation research on these iconic amphibians. [ABSTRACT FROM AUTHOR]