The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal whose populations have suffered a severe decline in recent decades. Its conservation requires a monitoring program to quantify changes in their populations and distribution. Scat surveys have usually been carried out for this purpose, but they tend to yield a low success rate, which depends on local environmental conditions such as channel form and lithology. This methodological constraint causes that part of the population goes unnoticed. In this study a new method for the detection of this elusive species is tested. The research has been done in the Basque Country (Northern Iberian Peninsula), in Elama and Leitzaran streams, where desmans have been recently recorded. Artificial shelters have been placed, regularly distributed in both streams, offering desmans suitable places to rest and defecate while foraging. The desmans used quickly and repeatedly the artificial shelters, significantly increasing their detection rate. The field identification of scats, based on their shape, colour, size and odour, was subsequently confirmed by DNA analyses with metabarcoding. This new non-invasive method allows obtaining fresh faecal samples of known age, making them available for further studies on genomics, population genetics, dietary studies, reproductive analyses, etc. The low cost of the materials used and the possibility of identifying desman scats after basic training, make this method optimal for synchronic, regional-scale and/or volunteer-based surveys. Thus, the use of artificial shelters results in a substantial improvement over traditional desman scat surveys, and greatly enhance the means for future monitoring of the populations of this endangered species.