Sambucus L. (Adoxaceae) has a rich fossil record with a major concentration in Europe and North Asia but a scarcity in relatively low latitudes of the Northern Hemisphere. Herein, we report fossil endocarps of the genus from the late Pliocene Heqing Basin of northwestern Yunnan, South China, which are assigned to two species, namely S. alveolatisemina and S. heqingensis Huang et Zhou sp. nov. Sambucus alveolatisemina has been formerly described from the similar geological horizon of the nearby Lanping Basin in northwestern Yunnan and possibly represents the fossil equivalent of S. adnata, an extant species commonly seen in this and neighboring regions. Sambucus heqingensis is newly erected due to its exceptionally slender endocarp shape together with the irregularly ridged endocarp surface and straight lateral margins. Our fossil discovery, in combination with the two fossil taxa from the late Pliocene Lanping Basin, suggests that the diversity of Sambucus might have risen in South China by the late Pliocene. We conclude that, as compared to Europe and North Asia, the distribution and diversification of the genus in South China with much lower latitudes is likely to be a recent event. This can be properly explained by the fact that Sambucus is generally a temperate element while the climate in South China in prior to the Pliocene might be too warm for its inhabitation. We propose a hypothesis that the colonization and diversification of the genus in other low-latitude regions of the Northern Hemisphere might have been similarly late in time.