Morphological and phylogenetic analyses were individually conducted for each commercial blackish Tuber from Yunnan Province, China. An internal transcribed spacer (ITS) phylogenetic analysis of Tuber ascocarps suggests that 3 phylogenetic clusters exist in Yunnan blackish truffles, which are the Indicum cluster, Formosanum cluster, and Pseudoexcavatum cluster. In total, 294 ITS sequences were obtained in 2017, among which 76% belonged to the Indicum cluster, 23% belonged to the Formosanum cluster, and 1% belonged to the Pseudoexcavatum cluster. Among the 10 ITS sequences obtained in 2016, 80% belonged to the Indicum cluster, and 20% belonged to the Formosanum cluster. The ratio of Indicum clusters to Formosanum clusters was approximately 4:1. Tuber ascocarps of the Pseudoexcavatum cluster were from Huize County; its members had a distinct morphology and could readily be distinguished from the others. Tuber ascocarps of Indicum and Formosanum clusters had no significant morphological differences, but a pairwise comparison suggested that their ITS sequences only shared 90.56~93.78% similarities. Blackish Tuber specimens from Gaoligong Mountain had a good aroma and were covered with soil containing metallic fragments; 75% of Tuber specimens from Gaoligong Mountain belonged to the Formosanum cluster.