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Coastal areas offer a diversity of habitats providing refugia and nursery for fish, promoting their biodiversity and associated contributions to people. Yet, natural coastlines are replaced by artificial infrastructures such as seaports and the influence of this artificialization on fish biodiversity remains poorly known. Here, we assessed fish biodiversity indicators using environmental DNA metabarcoding inside seaports and adjacent natural habitats including no‐take marine reserves. We found that species assemblages within seaports were primarily influenced by their area and habitat. We detected a similar species richness in seaports and reserves during lockdown, but seaports host more threatened species than natural habitats. Yet, species turnover between seaports was lower than between natural areas, reflecting biotic homogenization. Seaport managers should consider that complexifying artificial infrastructures could increase habitat diversity and coastal fish biodiversity. Our study illustrates that eDNA‐based indicators can be integrated in management and policy applications toward greener marine artificial infrastructures.