BackgroundSynotis (Asteraceae; Senecioneae) is a genus of about 55 species mostly distributed in the Sino-Himalayan region. During a botanical expedition in southwestern China in 2012, we found an unusual population of Synotis in southwestern Yunnan Province. To determine the taxonomic identity of the population, we carried out gross-morphological, floral micromorphological, and cytological observations.ResultsOur gross-morphological observations have shown that the population is most similar to Synotis auriculata C. Jeffrey & Y. L. Chen in leaf shape and in the number of phyllaries and florets, but readily distinguishable by the glabrous stem and petiole (vs. glandular pubescent), the exauriculate petiole (vs. auriculate), the uppermost leaves obviously smaller than the middle ones (vs. almost equally sized), and the larger ray florets (4–4.5 mm vs. ca. 2.5 mm). The floral micromorphological observations on the population agree with previous reports for other species of Synotis. The chromosomes of the population are counted to be 2n = 40. Its karyotype is formulated as 2n = 20m + 14sm + 6st.ConclusionsThe population was determined to represent a new species, i.e. Synotis baoshanensis M. Tang & Q. E. Yang, which is described herein. The species belongs to Synotis ser. Microglossae.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-17) contains supplementary material, which is available to authorized users.