Global losses of biodiversity are progressively increasing for many taxa during the Anthropocene. However, our ability to monitor biodiversity is reduced when dealing with elusive species, populations with low abundances, or remote locations. The analysis of DNA traces left by the organisms in the environment (eDNA) rose in the last decade as a promising approach to circumvent many of the challenges faced by other methods (e.g., audio-visual encounters and traps) traditionally used for monitoring species difficult to survey. The eDNA has the potential to improve our knowledge about species geographical distribution, population abundance and conservation status. Since 2014, we have applied the eDNA metabarcoding to: 1) test the feasibility of this approach for surveying water and ground dwelling amphibians in the Brazilian Atlantic forest; 2) compare the performance of traditional and eDNA methods for amphibian inventories; 3) search for DNA traces of 44 species reported to be declined or disappeared from the Brazilian Atlantic forest; and 4) identify the possible causes for these disappearances. We amplified around 50bp of 12S rRNA gene of amphibians from freshwater and leaf litter samples. Our results underscore the utility of eDNA metabarcoding as an efficient approach for surveying amphibians associated to tropical water bodies. However, it was not supported as a powerful approach for surveying ground dwelling species using leaf litter samples. The eDNA had a greater capacity of detection per sampling event than rapid field surveys, confirming the presence of species undetected by methods traditionally used. We successfully detected DNA traces of four declined species (Hylodes ornatus, Hylodes regius, Crossodactylus timbuhy, and Vitreorana eurygnatha); three locally disappeared (Boana semiguttata, Phasmahyla exilis and Phasmahyla guttata); and two species that have not been seen since 1982 (Cycloramphus cedrensis) and 1968 (Phantasmarana bocainensis). Our results underscore the efficacy of eDNA metabarcoding to survey species at low population densities and its potential application in conservation biology.