Mylopharyngodon wui, sp. nov., based on a completely preserved right pharyngeal bone with teeth from a middle Miocene deposit of the IVPP 346 Locality (43°24′53.4″N, 113°07′06.1″E) in the Tairum Nor area of Suniteyou Qi (Banner), Inner Mongolia, China, is described and compared with the living counterpart. It is different from the living black carp in having a generally smaller anterior angle, pharyngeal teeth a1 and a2 almost similar in size, and much rounder teeth a2 and a3. The ecological niche model of the living black carp, based on the Genetic Algorithm for Rule-set Production (GARP), shows that the fossil black carp is no longer in the niche model area, indicating that the regional environment has changed greatly, and that the black carp's niche has shrunk southeastward. The niche model also confirms that the distribution of the black carp is restricted by altitude above sea level. It may be inferred that the Inner Mongolia Plateau has risen more than 1000 m since the middle Miocene if the niche remained stable or evolved little over a long period of time.