Tsuga (Endl.) Carrière (Pinaceae) has a rich fossil record represented by pollen, leaves, wood and seed cones. Although fossil leaves of the genus have been widely documented, most of them have not been examined microscopically, which may limit their taxonomic resolution. In this study, three-dimensionally preserved leaves and leaf fragments of Tsuga from the Neogene (latest Miocene to Pliocene) Baoshan Basin in western Yunnan, southwest China, were examined both morphologically and micromorphologically. The fossil leaves are characterized by flattened and bifacial shape, round to obtuse apex and petiolate base, adaxially sunken and abaxially elevated midvein, adaxial surface without stomata and with elongated, smooth-margined epidermal cells, and abaxial surface with two stomatal bands along the midvein, each stomatal band consisting of 6–8 longitudinal stomatal lines. Based on comparisons with extant species of the genus, we found that the fossil leaves show the closest affinity to Tsuga dumosa (D. Don) Eichler, an extant species growing in the modern western Yunnan. As modern species of Tsuga prefer humid conditions, our fossil find suggests a humid climate in the Baoshan Basin at the time of fossil deposition, probably due to the influence of the Indian summer monsoon from the southwest. This is consistent with previous results of quantitative palaeoclimate reconstructions using spore/pollen fossil assemblages. Our study provides new fossil evidence for the origin of modern conifer diversity in southwest China. It highlights the importance of microscopic studies in the taxonomic resolution of fossil leaves of Pinaceae.