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Although tropical forests are among the most species-rich ecosystems on earth, 42% of mammal species in tropical forests are endangered because of overhunting and/or unsustainable exploitation. Camera-trap surveys have shown that natural saltlicks can be used to determine mammalian fauna, especially medium to large endangered species in tropical forests; establishment of camera traps, however, is time and effort intensive. Furthermore, the photographic range and detectable size of species are often restricted. Environmental DNA (eDNA) metabarcoding is a powerful approach that might provide a better way to study terrestrial animals in tropical forests. In this study, we examined whether eDNA from natural saltlicks comprehensively represented species composition in a Bornean tropical forest. We collected 100–150-mL water samples from natural saltlicks in Sabah, Malaysian Borneo. We constructed amplicon libraries for MiSeq sequencing using eDNA extracted from the water samples. Six endangered species were detected using this method, including Bornean orangutan (Pongo pygmaeus), Bornean banteng (Bos javanicus lowi), Asian elephant (Elephas maximus), Sunda pangolin (Manis javanica), sambar deer (Rusa unicolor) and bearded pig (Sus barbatus). However, most small and minor species were not detected, with low sequence identity (80–96%). Therefore, we propose that more species of tropical forest mammals should have their sequences deposited in DNA databases. This study is the first to report the endangered mammals of a tropical forest detected using eDNA from natural saltlicks.