Recent taxonomic revision of the strikingly ornamented millipedes known as ‘dragon millipedes’ in the family Paradoxosomatidae, has revealed generic division into six genera. The majority of species are distributed in mainland South-East Asia and each genus is restricted to a well-delimited area. However, their evolutionary history has remained poorly understood, particularly the relationships among genera and their biogeographic distribution. We present a comprehensive and well-resolved molecular phylogeny based on mitochondrial and nuclear genes. A dataset of 256 sequences representing 40 dragon millipede species was newly generated and analysed in order to reveal the relationships and to explore the origin using ancestral range reconstruction. All dragon millipedes were retrieved together as monophyletic, each genus except Hylomus forming a distinct clade with strong statistical values, supporting the previous classification using morphology. A new monotypic genus and new species, Siamaxytes bifurca Srisonchai and Panha gen. nov. et sp. nov., was revealed based on distinct morphological and DNA data. The Tenasserim mountain range was inferred to be the centre of origin of dragon millipedes with a series of subsequent diversifications across mainland South-East Asia. Our analysis provides evidence that both dispersal and vicariance presumably played a role in shaping these millipedes’ distribution and diversification.