The European weather loach (Misgurnus fossilis) represents one of many European freshwater fishes in
decline. Efficient monitoring is essential if conservation efforts are to be successful, but due to the species’
cryptic biology, traditional monitoring methods currently in use are inefficient, time consuming and
likely prone to non-detection error. Here, we investigate the usefulness of environmental DNA (eDNA)
monitoring as an alternative or supplementary method for surveying the Danish weather loach population, which is presumed to consist primarily of a single group of no more than 50 individuals. In 2008, the
majority of historical Danish localities were surveyed, using traditional fishing techniques. We then
applied eDNA methods to a number of these, as well as other potential localities. We successfully
detected the weather loach at multiple sites in the single known remaining locality; a result that was
later confirmed when local managers caught eight live specimens. Furthermore, the eDNA method indicated presence of the weather loach in another historical locality, where the species has not been
observed since 1995. At the remaining localities, weather loach eDNA was not detected, providing further
evidence for its absence. Importantly, the eDNA survey required less effort in person-hours and lower
costs than the traditional fishing survey. This study confirms that eDNA monitoring is a valid supplement
to traditional monitoring methods currently applied to monitor rare freshwater fishes. We propose that
by providing reliable distribution data at lower cost and limited effort, the eDNA method can allow for
increased management efficiency of endangered freshwater species such as the European weather loach.