Environmental <scp>DNA</scp> detection of three threatened stream frog species suggests widespread presence of two species and widespread loss of one

Abstract Amphibians face severe threats globally, with the amphibian chytrid fungus Batrachochytrium dendrobatidis causing drastic declines in many species, resulting in small remnant populations that can be hard to find. Environmental DNA (eDNA) methods offer a promising survey tool for detecting remnant populations, given detection sensitivity and ability to screen vast, remote areas. We conducted eDNA surveys for three stream frog species: the Critically Endangered Armoured Mistfrog ( Litoria lorica ), the Endangered Waterfall Frog ( L. nannotis ) and the Endangered Australian Lacelid frog ( L. dayi ). These inhabit the Wet Tropics World Heritage Area, north‐east Australia, and were heavily impacted by amphibian chytrid fungus in the 1980s and 1990s. We tested for the three species' eDNA in all catchments with historic records and adjacent catchments where they potentially occurred pre‐decline, using three species‐specific eDNA assays. Litoria lorica was only detected in samples collected 22 km downstream of the single known population. Litoria nannotis and L. dayi were detected across many catchments, including some with no records of the species post‐declines. The results support on‐foot survey results suggesting that L. lorica survived chytrid‐induced declines at a single site but reveal that L. nannotis and L. dayi are more widespread than thought, showing the value of eDNA methods in detecting remnant amphibian populations post disease declines.