Recent advances in molecular scatology have allowed the development of reliable and non-invasive methods that can be applied in monitoring of small carnivores, without disturbance of the animals. Here a method is described that can be used to differentiate European mink Mustela lutreola, polecat M. putorius and American mink M. vison based on the analysis of DNA extracted from faeces. It consists of a nested PCR of a region of the mitochondrial D-loop followed by digestion of the resulting 240 bp amplicons with the restriction enzymes RsaI and MspI. The restriction patterns of both enzymes, when used together, are found to detect species-specific sequence variation. Two different haplotypes for European mink (AA, AB), another two for the polecat (AC, AD) and one for American mink (BC) can also be discriminated by this technique. Two new haplotypes for the mitocondrial D-loop of mustelids are described after DNA sequencing.