Genetic Reference Gaps Limit eDNA Metabarcoding and Biodiversity Monitoring of Tropical Mangrove Ecosystems

ABSTRACT Mangroves support high faunal diversity and provide essential ecological services. However, biodiversity assessments in these habitats remain constrained by their structural complexity, resulting in limited accessibility, low visibility, and persistent taxonomic gaps. Rapid advances in molecular techniques use environmental DNA (eDNA) metabarcoding as an emerging, powerful alternative to conventional surveys. However, its effectiveness in tropical systems, such as Philippine mangroves, is constrained by gaps in publicly available genetic reference data, particularly for invertebrates. To address this, we systematically reviewed 48 years (1977–2025) of literature records of Philippine mangrove‐associated fauna and assessed their representation in public genetic databases to address three questions: (a) What is the current state of faunal biodiversity in Philippine mangroves? (b) How complete are public genetic reference libraries for eDNA applications? and (c) How can integrating eDNA with conventional surveys enhance ecological monitoring? We outlined a workflow for literature screening, taxonomic standardization, and programmatic retrieval and quality‐filtering of GenBank accessions. Across 999 species spanning nine phyla, the ray‐finned fishes (40.4%) dominated the records, followed by gastropods (21.7%) and bivalves (16.5%). Only 70.27% of species had at least one mitochondrial marker, dominated by COI (89.03%), followed by 16S (70.23%), 12S (60.97%), and Cytb (2.45%). Coverage was particularly low for invertebrates and some commercially important conservation‐relevant fishes, limiting species‐level detection in eDNA metabarcoding. Nevertheless, integrating eDNA with traditional methods increases the detection of cryptic, rare, juvenile, and hard‐to‐sample taxa, enabling more comprehensive biodiversity assessments. This combined approach enhances the capacity for spatial and temporal monitoring and supports more informed conservation strategies. Additionally, these data have the potential to enhance faunal assessments and strengthen biodiversity management practices. Overall, this review underscores the need to expand locally curated, voucher‐linked reference databases through targeted sequencing and highlights how national and regional partnerships can improve the accuracy and conservation relevance of eDNA‐based biodiversity monitoring.