Carnivores play a vital role in ecosystem health and are thus an important focus for conservation management. Non-invasive methods have gained traction for carnivore monitoring as they are often elusive and wide-ranging, making visual counts particularly difficult. Faecal mini-barcoding combines field collection of scats with genetic analysis for species identification. Here we assessed the applicability of a mini-barcode based on the mitochondrial ATP6 gene in southern Africa. We predicted amplification success based on in silico evaluation of 34 of the 42 terrestrial carnivore species existing in southern Africa, including the Congo clawless otter (Aonyx congicus) for which we contributed a mitochondrial assembly, and tested amplification success on available reference samples of 23 species. We expanded the existing ATP6 mini-barcode reference database by contributing additional sequences for 22 species including the Cape genet (Genetta tigrina) and the side-striped jackal (Lupulella adusta), for which no complete mini-barcode sequences were available on GenBank to date. We furthermore applied the ATP6 mini-barcode to a scat-based carnivore survey conducted in 2009 in a grassland habitat in Namibia, showing a 94.9% identification success. Six carnivore species were detected from157 samples and were predicted to account for 75% of species assemblage. Black-backed jackals (Canis mesomelas) contributed the majority of faecal samples (87.2%) and were distributed evenly throughout the area. Scat samples of the remaining species, including leopard (Panthera pardus), were distributed along the edge, in proximity to dense bushland.