Abstract:  Rescue excavations carried out from 2007 to 2010 at the Shuitangba lignite field in Zhaotong, Yunnan Province, not only resulted in the discovery of a new hominoid cranium and the addition of a new hominoid site in Yunnan, but the finding of a new muntjak with following characters: the brow tine is very close to the burr, which is moderately developed; the main beam extends backward and somewhat laterally, and then turns somewhat medially; and the neocrista and entocingulum are developed on the upper molars. The four limbs are relatively short. A cladistic analysis shows that the new materials represent a muntjak that is not in a sister-group relationship with Muntiacus leilaoensis from Yuanmou Late Miocene hominoid site, but rather represents an independent branch. Muntiacus zhaotongensis sp. nov. is proposed for the new muntjak materials. “Metacervulus sp.” from the “Yongle lignite field” recovered in 1978 is a synonym of the new species. The so-called “Yongle lignite field” is actually the Shuitangba lignite field. The layers yielding the materials of M. zhaotongensis sp. nov. are all within C3An.1n based on paleomagnetic correlation, with an estimated age between 6.1 to 5.9 Ma (terminal Miocene).