We estimated the phylogenetic relationships of an enigmatic small toad Parapelophryne scalpta from Hainan Island, China to nine other bufonid genera from Southeast and East Asia using ca. 2000 bp sequences of the mitochondrial DNA genes 12S rRNA, tRNA^val, and 16S rRNA using maximum likelihood and Bayesian inference methods. The East and Southeast Asian bufonid genera formed a clade in which seven lineages with unresolved relationships to each other were recognized. Monophyly was supported only for (A) Parapelophryne and Bufo, (B) Phrynoidis and Pedostibes, and (C) Leptophryne and Ansonia. All genera were genetically divergent from each other and Parapelophryne, erected purely based on morphology, could be recognized as a distinct genus. On the other hand, it was found to be the sister genus of East Asian Bufo, an unexpected result given their great morphological difference and discontinuous distribution.