Anthracotheres were an environmentally sensitive group that were thought to have become extinct from the middle-high latitudes of the northern hemisphere by the early Miocene. Hereby, the present author reports previously unpublished fossil bothriodonts, a group of anthracotheres, from the northern Junggar Basin, in China’s far northwest. An M3 of a small bothriodont Elomeryx sp., from the lower part of the Halamagai Formation, which is probably of the early middle Miocene age, is the only anthracothere record from the Neogene of northern China. More importantly, it is the latest anthracothere record from the middle-high latitudes of the northern hemisphere. The other teeth from Xiaerhete locality of the Irtysh River Formation, which is of the late Eocene age, are identified as Bakalovia sp. This poorly known genus was previously only reported from the middle or late Eocene of Southwest Europe. This study complements the sparse anthracothere fossil records of northwestern China. The present material, together with previous records, strongly suggests the occurrence of anthracothere interchanges between East Asia and both Europe and North America possibly from the middle or late Eocene to the early Oligocene. Anthracotheres declined remarkably in the Oligocene and Miocene in northern China, in contrast to their continued abundance in South and Southeast Asia at the same time, suggesting the existence of climate zonation and a faunal discontinuity in mammal distribution patterns between the northern and southern China. This zonation was probably related to the uplift of the Tibetan Plateau, which altered atmospheric circulation throughout Eastern Asia.