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The brown hyaena Hyaena brunnea is a near threatened large carnivore inhabiting sub-Saharan Africa. Like many other species of terrestrial carnivores, brown hyaenas often and repeatedly deposit scats at specific latrine sites as a means of olfactory communication. However, previous studies on brown hyaena latrine use have been constrained to the arid Kalahari region in southern Africa, an area of low resource abundance. To improve our understanding of geographic variation in the biology of this species, we monitored patterns of brown hyaena scat deposition in the Waterberg of northern South Africa, an area of higher net productivity than previous areas for published brown hyaena studies. Defecation rates at latrine sites were low in our study area (median: < 1 defecation in 30 days), but brown hyaenas visited sites significantly more often than they defecated at them (median: 2.6 visits/30 days). The temporal patterns of activity at defecation sites were significantly related to the overall temporal activity patterns of brown hyaenas on the roads within the reserve, and generally confirmed a nocturnal activity pattern in the species. Our result on brown hyaena scat deposition in the Waterberg region indicates a geographic variation in latrine use, and we suggest that such a variation could be linked to resource-driven variation in social and spatial organisation.