Natural hybridization can impact species diversity as an important evolutionary process and it is very common in Begonia, a mega-diverse plant genus. Recently, a natural hybrid between Begonia palmata and B. circumlobata was found in three locations of southeast China. It is very similar to B. palmata and difficult to identify only based on morphological characters. According to the maternal uniparental inheritance of chloroplast genome and biparental inheritance of nuclear genome in Begonia, nuclear locus (ITS) and chloroplast loci (rpL16) phylogenetic trees were constructed for the putative hybrid and its parents. The results indicated that the putative hybrid is an F1 generation with B. palmata mostly as maternal parent and B. circumlobata as paternal parent. The hybrid is described and illustrated as a new species (Begonia × yueminensis D.K.Tian et C.Z.Yang), and it is morphologically compared with its allied species.