Melia L. is a small genus of only 2–3 species, which is native to Indo-Malesia, India, Pakistan and southern parts of tropical Africa. Fossil records of Melia are known from the early Miocene to the Pleistocene. Here we describe some mummified fossil endocarps of Melia from the upper part of the Yongning Formation (late Oligocene) in Nanning Basin, South China. These well-preserved stony endocarps are 8–14 mm long and 5–9 mm wide, and have 5 locules with a single spindle seed per locule. We interpret these endocarps as the internal remains of a Melia drupe, and assign them as a new species:M. santangensis sp. nov. This is the only fossil record of anatomically preserved Melia found in China, and also the oldest fossil record of Melia so far reported globally. The fossil record confirms the presence of Melia in Asia at the late Oligocene, and provides evidence supporting the distribution and dispersal hypothesis of the Meliaceae.