Bryophytes play an important role as habitats for many organisms, especially invertebrates, however, few studies have focused on understanding the cryptic ecosystems associated with them. The use of molecular tools allows for advances in diversity assessment of environmental samples. In particular, the use of DNA metabarcoding is an efficient method for detection of the DNA of rare and cryptic species, including resting stages typically undetected in morphological surveys. We used DNA metabarcoding to investigate the hidden diversity present in two moss carpets in the largest of the world’s remaining rainforests, the Amazon. More specifically, our samples took place in the Brazilian state of Amapá, the least affected by anthropogenic pressures. Samples, 10 m apart, were collected under sterile conditions and eDNA was extracted. To maximize diversity coverage, three regions were sequenced (ITS2, COX1 and 16S). A total of 348 taxa were assigned from the sequences obtained, with 123 eukaryotic taxa representing five Kingdoms assigned from COX1, 64 representing four Kingdoms from ITS2 and 161 representing one prokaryotic Domain from the 16S region. A total of 38% of taxa were Fungi, 35% Bacteria and 27% non-fungal eukaryotes. The data obtained highlight the importance of moss carpets providing habitats that support diverse communities. Given the high number of unassigned sequences, the available sequence databases for Amazonian species require improvement. As the region faces multiple threats, there is an urgent need for improvements in collection, identification ability, sequencing and DNA curation. There were several assignments of disease-causing organisms, this highlights the need for monitoring changes in these under-researched habitats. Keywords: bryophyte; high throughput sequencing; one health; cryptic diversity; environmental DNA; tropical rainforest. [based on the sequence ITS2 Absconditella rubra (= Absconditonia) rubra is listed as occurring in Amazonia]