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Yellow chanterelles are one of the most common edible mushrooms found in Yunnan Province, China. Previous studies identified the species of these mushrooms as Cantharellus cibarius Fr. based on morphology alone. However, the diversity of yellow chanterelles comprises many species within the C. cibarius complex, including C. yunnanensis W.F. Chiu. We hypothesized that the latter species is widely marketed in Yunnan Province and does not actually belong to C. cibarius. Hence, to confirm the species identity, taxonomic re-evaluation using integrated taxonomic approaches is required. Herein, samples collected from different markets and from near the type locality were subjected to morphological and molecular analyses. We generated tef-1α sequences and analyzed them using the maximum likelihood and Bayesian inference methods. The study revealed that the specimens previously identified as C. cibarius with a wide distribution in southwestern China are indeed C. yunnanensis. Our morphological assessment was markedly influenced by the revision of the type specimen (C. yunnanensis) and its original description, as some characteristics of the specimen did not match the description (e.g., the size and shape of the spores). Similarly, our single-locus phylogenetic analysis strongly supported the identification of the marketed species in Southwestern China (Guizhou and Yunnan Provinces) as C. yunnanensis instead of C. cibarius. Following our findings, we epitypified C. yunnanensis. Additionally, we collected, identified, and confirmed the presence of C. cibarius in northeastern China.