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.

California’s Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores – and their microbiomes – in island environments.