Our understanding of the flora of China has greatly improved during the last 100 years but effective management of the rich biodiversity and unique natural resources requires resolving the taxonomic limitations of existing treatments. Here, we focus on the epiphytic genus Scleroglossum with special emphasis on the occurrences in Hainan and Yunnan of mainland China. By combining fieldwork, herbarium studies, and DNA barcoding we test the hypothesis that this genus is represented by more than one species in China. Our integrative results show the Yunnan accessions are distinct from those in Hainan in both phenotypic and genotypic variation. The Yunnan accessions belong to S. pusillum, whereas the Hainan accessions represent a distinct species displaying the morphological characteristics of S. sulcatum. Genotypic evidence suggests the occurrence of cryptic diversity among accessions with the morphology of S. sulcatum. In summary, the study contributes to the crucial assessment of the plant diversity in Yunnan and illustrates the importance of integrating collection efforts and DNA barcoding approaches to enable effective assessment of the epiphytic diversity of Yunnan.