Three fossil species of Equisetum (Equisetaceae) were reported from the Neogene of south-western China and northern Vietnam, based on well-preserved rhizomes with tubers. Equisetum cf. pratense Ehrhart from the middle Miocene of Zhenyuan County, Yunnan Province, China is characterised by a bunch of three ovate tubers with longitudinal ridges on the surface. Equisetum yenbaiense A.T. Aung, T. Su, T.V. Do & Z.K. Zhou, sp. nov. from the late Miocene of Yenbai Province, Vietnam is characterised by four bunches of elongate tubers arranged in a whorl on a node. Equisetum yongpingense A.T. Aung, T. Su & Z.K. Zhou, sp. nov. from the late Pliocene of Yunnan is characterised by fibrous roots on most nodes and two to four bunches of large cylindrical tubers arranged in a whorl on a node. Floristic assemblages suggest that these species might have grown near a riverside or lakeshore. These new fossil records improve our understanding of species richness of Equisetum and their distribution range during the Neogene in Asia.