The publication – addressed to environmental consultancies, federal and cantonal agencies, as well as researchers – provides an introduction to the new techniques and an overview of the latest developments and possible applications. While advances in eDNA analysis are ongoing, the adoption of standard methods should ensure that scientifically reliable results can be obtained today. Case studies, detailed protocols and established practices should facilitate eDNA sample processing and enhance the comparability of eDNA methods. Finally, the guidelines should lead to harmonised enforcement practice and promote compliance with the relevant legal requirements on biodiversity monitoring across Switzerland. The new guidelines were prepared, under the aegis of the FOEN, by Eawag in collaboration with the Universities of Zurich and Geneva.