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The morphology of the amphibian skeleton is known to be influenced by a set of heterochronic processes, mostly related to paedomorphosis. Certain paedomorphic underdevelopments, such as reduction of some cranial and postcranial bones, are believed to accompany the trend of body miniaturization. At the same time, the role of reproductive mode and life history in the skeletal development in amphibians is also widely recognized. The anuran family Microhylidae is a speciose and diverse taxon encompassing frogs of various sizes, from rather large to extremely miniature, and with various reproductive modes. Thus, microhylids represent a good model system to study diversification of skeletal morphology and development. Using ontogenetic series of larvae, metamorphs, and adults, we compared osteology in frogs from the genera Glyphoglossus, Microhyla, Kalophrynus, and Kaloula from Southeast Asia (Vietnam). To estimate the impact of miniaturization, skeletal structure and development were compared in the most large- and small-sized species. In the latter, adult osteology was revealed to be affected by the pattern of larval development rather than miniaturization per se. As compared with typical pond-breeders, in hole-breeding Microhyla arboricola with oophagous tadpoles, reduction of cranial elements (columella, quadratojugal) and vertebrae count (6 presacral vertebrae instead of 8) presumably results from the heterochronic shift in the timing of bone formation. Abbreviated larval development in the medium-sized Kalophrynus interlineatus, which breeds in ephemeral pools, accounts for the underdevelopment of the skeleton in metamorphs and loss of some bones in adults (palatine, sphenethmoid). These findings suggest that the ecology of reproduction and life history traits play a key role in the formation of the skeleton in frogs.