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Sorbus setschwanensis Koehne is a pinnate‐leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein‐coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR‐atpA, petN‐psbM, ndhC‐trnV, trnE‐trnT, trnT‐trnL and rpl32‐trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied.

Eight taxa of Sorbus Linnaeus, 1753 sensu stricto (Rosaceae) from China have been studied karyologically through chromosome counting, chromosomal measurement and karyotype symmetry. Genome size was also estimated by flow cytometry. Six taxa, S. amabilis Cheng ex T.T.Yu et K.C.Kuan, 1963, S. hupehensis var. paucijuga (D.K. Zang et P.C. Huang, 1992) L.T. Lu, 2000, S. koehneana C.K. Schneider, 1906, S. pohuashanensis (Hance, 1875) Hedlund, 1901, S. scalaris Koehne, 1913 and S. wilsoniana C.K. Schneider, 1906 are diploids with 2n = 34, whereas two taxa, S. filipes Handel-Mazzetti,1933 and S. ovalis McAllister, 2005 are tetraploid with 2n = 68. In general, the chromosome size is mainly small, and karyotypes are symmetrical with predominance of metacentric chromosomes. Genome size variation of diploids and tetraploids is 1.401 pg –1.676 pg and 2.674 pg –2.684 pg, respectively. Chromosome numbers of S. amabilis and S. hupehensis var. paucijuga, and karyotype and genome size of eight taxa studied are reported for the first time. This study emphasised the reliability of flow cytometry in genome size determination to infer ploidy levels in Chinese native Sorbus species.