Pinus prekesiya Xing, Liu et Zhou sp. nov. was described as a new species on the basis of two well preserved ovulate cones from the upper Miocene of central Yunnan, southwestern China. It is the first fossil record of three dimensionally preserved Pinus ovulate cones from China. Morphological comparisons with 15 previously published Cenozoic cones and seven related extant pine species reveal that the fossil cones are identified as a new species, P. prekesiya sp. nov., which belongs to subsection Pinus of subgenus Pinus. The new species shows a combination of characters of P. kesiya and P. yunnanensis, but has a closer affinity with P. kesiya which occurs in the humid region of Yunnan and therefore suggests a more humid climate in central Yunnan during the late Miocene than today. The general cooling trend during the late Neogene and topographic change due to the dramatic Tibetan uplift might have caused a vicariant origin of P. kesiya and P. yunnanensis from the ancestral P. prekesiya.