Fish Community Composition Revealed by eDNA Metabarcoding in Mangrove‐Associated Lagoons of Negombo and Puttalam, Sri Lanka

Mangrove‐associated lagoons are critical nursery and feeding habitats for fishes, yet their biodiversity in Sri Lanka remains poorly documented due to reliance on conventional, catch‐based methods. Here, we applied environmental DNA (eDNA) metabarcoding to characterize fish assemblages in Negombo (wet zone) and Puttalam (dry zone) lagoons. Next‐generation sequencing of eDNA extracted from water samples yielded over 1.68 million quality‐filtered reads, which were assigned to 194 operational taxonomic units (OTUs). These OTUs represented 87 species from 47 families in Negombo and 54 species from 35 families in Puttalam, with 39 species shared between the lagoons, the majority of which were euryhaline. Relative read abundance profiles revealed greater spatial heterogeneity in family composition within Negombo, whereas Puttalam was characterized by stronger dominance of a smaller number of fish families. Shannon diversity was highest at the lagoon mouth and lowest in the inner lagoon in both systems. Beta diversity analyses revealed a significant difference in fish community composition between the two lagoons (PERMANOVA, R 2 = 0.106, p = 0.001), whereas no significant differences were detected among regions within lagoons. Species richness estimates were broadly comparable to historical records based on conventional surveys. However, eDNA metabarcoding provided complementary insights by detecting a wider range of commercially important, cryptic, and reef‐associated taxa. These findings demonstrate the utility of eDNA metabarcoding for characterizing fish communities across marine–brackish–freshwater transitions. Our study provides an updated molecular‐based assessment of fish diversity in Negombo and Puttalam lagoons and highlights the potential of eDNA for biodiversity monitoring and fisheries management in Sri Lanka's coastal ecosystems.