Ophiopogon Ker-Gawl. (Ophiopogoneae, Asparagaceae) is a genus containing approximately 65 species distributed in East and Southeast Asia. The biogeographical history within the area is still poorly known. Divergence time estimation was used to infer the biogeographic history of Ophiopogon based on nuclear ribosomal internal transcribed spacer data from 33 Ophiopogon species, three Liriope Lour. species, and six Peliosanthes Andrews species. The ancestral area and dispersal routes of Ophiopogon were inferred using the Bayesian binary method. Ophiopogon motouensis S. C. Chen was a transitional taxon. Ophiopogon was estimated to have originated in Southwest China during the middle Miocene (11.74 Ma). Five migrations were hypothesized to explain the expansion of Ophiopogon from Southwest China to East China, South Central China, South China, Taiwan, and Southeast Asia. The separation of Ophiopogon into East China and South Central China may be consistent with a broad east-west arid zone in continental Asia during the Paleogene. A migration from Southwest China to Taiwan was inferred in the Pliocene, when the ancestor of O. intermedius D. Don may have moved from Southwest China through the Yunnan-Guizhou Plateau by the Nanling Corridor and Fujian-Taiwan Bridge into Taiwan. There was a dispersal route in the Pliocene (at 3.79 Ma) from Southwest China to South China, either along the Taiwan route (from Southwest China through the Yunnan-Guizhou Plateau along the Nanling Corridor to Guangxi), or related to the E'mei Mountain orogeny. There was another dispersal event in the early Pleistocene at 2.00 Ma from Southwest China to Southeast Asia, possibly associated with the last uplift of the Qinghai-Tibetan Plateau.