Frogs of the genusMicrohylainclude some of the world’s smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genusMicrohylaremains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorialGlyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genusMicrohyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominalMicrohylaspecies and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: theGlyphoglossusclade, Southeast AsianMicrohylaII clade (includesM. annectensspecies group), and a diverseMicrohylaI clade including all other species. Within the largest major clade ofMicrohylaare seven well-supported subclades that we identify as theM. achatina,M. fissipes,M. berdmorei,M. superciliaris,M. ornata,M. butleri, andM. palmipesspecies groups. The phylogenetic position of 12 poorly knownMicrohylaspecies is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show theMicrohyla—Glyphoglossusassemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. WhileGlyphoglossusandMicrohylaII remained within their ancestral ranges,MicrohylaI expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of fiveMicrohylaspecies groups independently, starting with the end Oligocene—early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups ofMicrohylahave independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallestMicrohylaspecies are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases inMicrohyla—Glyphoglossusseem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity inMicrohylaand reveal 15–33 undescribed species. We revalidateM. nepenthicola, synonymizeM. pulveratawithM. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.