Understanding marine surface fish diversity is crucial for ecosystem management. However, the traditional sampling methods are often invasive, costly, or unsuitable for certain species or locations. Environmental DNA (eDNA) metabarcoding provides a non-invasive and relatively cheap alternative to explore patterns of diversity. It is important to recognize that, eDNA-based inference can vary across sampling methods, potentially impacting the validity of biodiversity assessments. To evaluate and compare the effectiveness of three eDNA sampling methods—ship-bottom intake (4.5 m), Niskin bottles (5 or 10 m), and bucket (0 m)—for assessing fish diversity and fish community composition in the western North Pacific near Japan, we analyzed fish communities from 83 stations sampled during nine research cruises. Taxonomic analysis revealed that each method detected over 324 taxa, contributing to a total of 465 taxa. Hierarchical clustering generally identified similar species composition across methods at a station. The exception was when intake samples, collected at different times, diverged from bucket and Niskin samples at the same station. Hill’s number rarefaction and extrapolation curves across all clusters showed similar results among methods, with exceptions in a few clusters where bucket samples exhibited higher biodiversity indices than intake and Niskin samples. Non-metric multidimensional scaling indicated significant relationships between cluster composition and environmental factors like temperature, salinity, and chlorophyll-a. Some clusters were also controlled by integrated seasonal factors. Overall, fish community composition was convincingly similar among methods. This finding suggests that any of these eDNA sampling methods can be effective and may be prioritized based on logistical considerations.

The distribution of fish larvae in estuaries is crucial for comprehending the functioning of these ecosystems and their role as nursery grounds for marine fish species. Data regarding larval fish assemblages in the coastal waters of Bangladesh are currently scarce. This study examines the spatial and seasonal dynamics of larval fish communities in these waters using a two-year sampling effort with a bongo net. This study investigates the diversity, abundance, and distribution of larval fishes at four sites (Bakkhali River Estuary, Moheshkhalipara, Naf River Estuary, and Rezu Khal Estuary) on the southeastern coast of Bangladesh. A total of 10,387 fish larvae representing 25 families were identified. Clupeidae (42.9%), Engraulidae (35.5%), Ambassidae (10.1%), Myctophidae (2.1%), and Gobiidae (1.9%) were the five most dominant families based on the larval catch composition. Marked seasonal differences in the larval fish abundance were observed. However, these differences were not observed when comparing the four sampled sites. Additionally, the correlation between environmental variables and the larval abundance indicated that salinity negatively influences (p < 0.001) the larval fish abundance. This is the first comprehensive investigation of larval fish assemblages in the coastal waters of Bangladesh. The findings of this study enhance our understanding of the nursery habitat requirements for the early development stages of both migratory and resident species in subtropical coastal waters, providing valuable information for potential applications in management and conservation efforts.

Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web‐based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line—believed to exist along a geographic canyon known as the Tokara Gap—were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun‐inoue/eDNAmap .