Yunnan, southwestern China, represents a modern biodiversity center for Rubus (Rosaceae). The history for this high modern diversity remains poorly known due to the lack of fossil evidence. In this report, fossil pyrenes of Rubus are taxonomically studied from the late Pliocene (Piacenzian) of Lanping County, northwestern Yunnan. These pyrenes show a greater morphological variation than that of extant Rubus pyrenes within the same species, indicating that they belong to different taxa of Rubus. Based on comparisons with both modern and other fossil species, our fossil pyrenes are assigned to five taxa, including a newly established one, Rubus lanpingensis nov. sp. These fossils suggest a somewhat high species diversity of Rubus in Lanping, a small area in northwestern Yunnan, during the late Pliocene. This provides the first fossil perspective for an understanding of the historical background of the modern Rubus diversity in a limited geographic area of Yunnan. The inferred palaeobiodiversity is probably associated with a large environmental heterogeneity in a limited area of Yunnan at that time.