Metabarcoding – taxon identification from complex mixtures using a standard DNA region – is increasingly used in evolutionary studies. With this method, it is not only possible to delimit species or collect indirect observational data but also to determine diets. Caveats such as false negatives and skewed abundances can be overcome when metabarcoding is combined with traditional methods such as microscopy. Such a combined approach can help deducing why some species went extinct or became endangered whereas others evolved into new lineages. This review will focus on the added value of metabarcoding when combined with traditional methods for evolutionary studies of mammals.