Studies on the evolutionary history of Neotropical dung beetles have revealed a complex process of speciation since the Cenozoic. We use Late Pleistocene fossil records to contribute to our understanding of large-scale temporal changes in their biodiversity. Based on these records, we describe Pleistoaphodius mariopinoi gen. et sp. nov. a new small dung beetle (Scarabaeidae, Aphodiinae, Aphodiini) from southern Chile. Comparative morphology supports its placement within the tribe Aphodiini and reveals its closest affinities being to the extant genus such as Gordonius, Haroldiellus, and Neodiapterna. This discovery expands the diversity of Quaternary dung beetle assemblages in southern South America, highlighting that local Aphodiinae were more diverse prior to the Pleistocene-Holocene transition. Additionally, we analysed the biogeographic patterns of this extinct assemblage of dung beetles and their related extant species. Our findings support the hypothesis that the current distribution and abundance of South American dung beetle species have been largely influenced by the extinction of megafauna during the Pleistocene-Holocene transition.