The biota of mangrove ecosystems can now be evaluated using environmental DNA (eDNA). By characterizing the spatio-temporal distribution of eDNA, metabarcoding provides a non-destructive method to monitor coastal biodiversity, particularly in mangrove forests. Given the availability of biodiversity data, the resilience of coastal ecosystems can be enhanced through efficient data-driven coastal management. As a milestone, UNESCO launched a project to understand biodiversity richness based on eDNA methods to monitor fish and IUCN Red List species from selected marine world heritage sites.

Recent observations confirm that eDNA can be used to monitor IUCN-designated threatened taxa in tropical mangrove ecosystems, and the results of this technique are highly important for providing information on conservation priorities. Using environmental DNA as the primary technique for biomonitoring in mangrove environments can offer solutions for the sustainable development of coastal biological resources.

Terrestrial, aquatic, and intertidal fauna found in mangrove forests exhibit diverse life history strategies and may use mangroves for part or all of their life cycles. Taxon detection depends on many factors, such as tidal conditions, seasonal climate, salinity gradients, and water column stratification. Furthermore, understanding the processes that regulate the release of eDNA from focal mangrove fauna and its removal in the intertidal environment is crucial.

Dynamic spatio-temporal heterogeneity in mangrove fauna utilization also poses scaling challenges in defining sampling boundaries for different ecological and ecosystem applications. Due to the geomorphological complexity of mangrove habitats, species distribution data may be influenced by microhabitats, estuarine positions, biogeographic regions, and mangrove types. Therefore, eDNA metabarcoding studies in mangroves must include sampling at multiple spatial scales to enable a better understanding of species distribution. Consensus on sampling protocols at consistent scales is needed to facilitate comparative studies across mangrove ecosystems worldwide.