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Background  Continental China is the center of  Begonia  species diversity in Asia and contains more than 60 species out of about 110 named species of section  Platycentrum . Mt. Jinyun, located in Chongqing City at the upper reaches of the Yangtze River, harbors a subtropical broadleaved forest with high species diversity. During a botanical survey in Mt. Jinyun, an unknown  Begonia  species of sect.  Platycentrum  with palmately compound leaves was collected and studied based on detailed morphological observations and cytological and molecular phylogenetic analyses.    Results  The unknown  Begonia  bears a superficial resemblance to  B. hemsleyana  in having palmately compound leaves, a feature unseen in other species of sect.  Platycentrum  in China. It is however sharply distinct from the latter in the acaulous habit with aerial stems seen only at anthesis and long rhizomes (vs. erect stems to 70 cm or taller with short rhizomes), 4–6 pinnatilobed leaflets with indistinct, decurrent petiolules (vs. 7–10 serrate leaflets with distinct petiolules), and white (vs. pink) tepals. Molecular phylogenetic analyses based on nuclear ribosomal DNA and chloroplast DNA sequences indicated that this species was allied to  Platycentrum  species occurring in Southwest and South-central China and Vietnam, including  B. hemsleyana , and clearly separable from these species. Somatic chromosome number of 2 n  = 22 was reported for this unknown species. The diploid chromosome number is agreeable with those published for  Begonia  sect.  Platycentrum .    Conclusions  The unknown  Begonia  is confirmed to be a new species of sect.  Platycentrum  and hereto described as  Begonia jinyunensis  C.-I Peng, B. Ding & Q. Wang.    Electronic supplementary material  The online version of this article (doi:10.1186/s40529-014-0062-6) contains supplementary material, which is available to authorized users.

Begonia jinyunensis (Begoniaceae, section Platycentrum), a new palmately compound leaved species from Chongqing, China