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Estuarine and coastal ecosystems are important habitats for many fish species. Large-scale patterns of estuarine and coastal fish communities can be affected by geographical factors, such as water temperature and latitude, that limit or allow fish dispersal, and/or by environmental factors that select locally adapted species. Furthermore, increased human activity has also altered fish diversity by modifying estuarine/coastal environments. Here, we used environmental DNA metabarcoding to study a large-scale pattern of estuarine/coastal fish communities across 25 watersheds in the Japanese Archipelago, and we assessed the effects of geographical, environmental, and anthropogenic factors in structuring these communities. Of the 290 fish species detected, 47 species were red-listed by the Japanese Ministry of Environment, and nine were alien. Non-metric multidimensional scaling showed that latitude and water temperature affected both river-mouth and coastal-sea fish communities. Although other anthropogenic factors did not affect these communities, bank artificialisation rates influenced both. The relationship between each fish community and ocean currents was weak. The number of red-listed fish affected both fish community structures, whereas that of alien species did not. The numbers of red-listed fish in coastal points and of all fish species were negatively influenced to the human population density. These findings provide useful information that may be used to conserve estuarine and coastal ecosystems.

With broad distributions, diadromous fishes can be exposed to multiple threats at different stages of development. For the primarily catadromous eels of the family Anguillidae, there is growing international concern for the population abundance and escapement trends of some of these species and yet incomplete knowledge of their remarkable life-histories hampers management and conservation. Anguillids experience a suite of pressures that include habitat loss/modification, migration barriers, pollution, parasitism, exploitation, and fluctuating oceanic conditions that likely have synergistic and regionally variable impacts, even within species. In beginning to redress this rather fragmented picture, we evaluated the extinction risk of these species using the IUCN Red List of Threatened Species Categories and Criteria to infer population-wide trends from catch and monitoring data. Here we consolidate and build upon these species assessments by presenting an overview of the current state of global eel data and conservation, categorising the knowledge gaps and geographic regions where resources are needed and discussing future recommendations to improve our understanding of anguillids. We find stark disparity between the quality and length of data available to assess population trends and conservation priorities in temperate and tropical anguillids. Of the 13 species assessed, four were listed as ‘Threatened’ (Vulnerable, Endangered or Critically Endangered); four were Near Threatened, three were Data Deficient and two were deemed Least Concern. Comparing with other diadromous species, we examine the multiple threats that impact eels during their different life-history stages, highlighting the challenges of applying the Red List Categories and Criteria to geographically-expansive, catadromous and panmictic groups of species.