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Fossil spores of coprophilous fungi preserved in lake and bog sediments are well-established palaeoecological tracers for the local history of pastoralism and other animal husbandry. However, applications in Africa are limited by the lack of information on the exact relationship between human activity and fungi growing on large-herbivore dung. Here we use 25 small crater-lake basins in western Uganda, which cover the complete regional gradient of natural vegetation and human impact intensity, as a natural laboratory to assess the relationship between coprophilous fungal spores recovered from recently deposited bottom sediments and the presence and abundance of large domestic herbivores in the surrounding crater basins. We find that the summed abundances of Sporormiella, Sordaria, Podospora and Delitschia, or of these four types plus Cercophora, are the most useful and robust fungal-spore indicators for the presence of domestic large herbivores in an East African context. Chaetomium could also be added to this list, particularly as it may help reduce stochasticity in the often low fossil counts of obligate coprophilous types. Our results suggest that domestic large herbivores, at least when associated with some degree of crop agriculture, leave a clearer signature on fungal-spore assemblages in the lakes’ sediments than large wildlife. Furthermore, they indicate that the typically small number of livestock kept by mixed-subsistence farmers leave a stronger imprint on fungal-spore assemblages than the much larger herds of specialist pastoralists occasionally visiting the lake to drink or bathe.