Severino G. Salmo, Arizaldo E. Castro, Kenneth Angelo Bagay, Marie Christine M. Obusan
ABSTRACT This study explored eDNA metabarcoding in the assessment of biodiversity in mangrove sediments across different stand types (i.e., natural, restored, and recolonized) in Prieto Diaz, Sorsogon (northeastern Philippines). Sediment samples were collected from 18 plots. The recovered sequences were analyzed using universal COI and 18S rRNA gene markers. A total of 18 unique species and 12 phyla were recorded across all sites. Community diversity metrics revealed a clear ecological gradient, with the highest diversity observed in recolonized mature stands, intermediate in the natural stands, and lowest in the restored stands. Taxonomic profiles varied with mangrove stand, age, and zonation. Recolonized sites hosted diverse community assemblies including fishes (Chordata), polychaetes (Annelida), diatoms (Bacillariophyta), and sponges (Porifera), while restored sites were dominated by nematodes. Principal component and co‐occurrence network analyses revealed associations between specific taxa and stand types. Positive species correlations suggest association with mangrove conditions, while negative associations may be indicating niche partitioning. This study demonstrated the utility of sediment eDNA metabarcoding as a minimally invasive approach for capturing community‐level biodiversity in mangroves. It complements traditional monitoring approaches and can inform restoration, impact assessments, and conservation planning. Limitations such as taxonomic resolution highlight the need for optimizing and expanding metabarcoding efforts in the Philippines and in Southeast Asia. Our findings reinforce the importance of habitat complexity and recolonization in the restoration of mangroves while demonstrating the advantages (and disadvantages) of eDNA‐based assessment techniques.