eDNA sampling is a more affordable, quick, and consistent method to understand the aquatic ecosystem, especially the ocean, with freely associated DNA in water suitable for estimating diversity, composition, and behaviour. Furthermore, it helps to propose management plans to use sustainable ocean resources. The world's mangroves are currently under threat, and they also provide habitat for International Union Conservation of Nature (IUCN)-listed threatened species (e.g., Dugong, Bengal Tiger, etc.). These species are inextricably linked to the mangrove ecosystem, forming a sustenance chain that can be disrupted if lost. On the other hand, the more reliable methods to monitor threatened species are not clearly established and mostly depend on the non-standardized method, which requires practical and taxonomic expertise and limits the data-driven conservation acts. The implementation of eDNA in ocean data collection and monitoring of endangered species is still in a progressive stage and the studies on the eDNA of threatened species from mangrove ecosystems are few. Environmental DNA surveys have also mapped the distribution of endangered European eel (Anguilla anguilla) during spring and documented threatened sharks and rays across eastern Indonesia. As a hallmark, UNESCO recently launched a project to understand the richness of biodiversity. The main objective is to monitor fishes, including the IUCN red-listed species, through eDNA collected across the selected marine World Heritage sites. The recent observations ensure that eDNA might be used to monitor the IUCN-designated threatened taxa found in the tropical mangrove ecosystem. The outcomes of this eDNA technique are crucial for providing information regarding conservation priorities.