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Abstract We investigated the biogeography of benthic foraminifera in a highly urbanized tropical seascape, i.e. Hong Kong, in order to assess their utility as bioindicators relative to other marine fauna. Hong Kong is one of the largest coastal cities on the planet and studies of other benthic fauna in the region are available for comparison. We found that: (1) turbid, muddy habitats host a unique foraminiferal fauna; (2) areas with intermediate levels of eutrophication have the highest foraminiferal species diversity; (3) semi-enclosed and heavily polluted environments host a distinct foraminiferal fauna, characterized by low taxonomic diversity and/or high dominance, and that is acclimated to stressful marine conditions. Biodiversity patterns of foraminifera in Hong Kong are generally consistent with those of other soft-sediment macro- and meio-fauna (e.g. polychaetes, molluscs and ostracods); however, foraminifera may be more sensitive than these other groups to eutrophication and associated changes in coastal food webs. The tolerance of some, but not other, species to eutrophic and hypoxic conditions means that foraminiferal faunas can serve as bioindicators across a wide array of environmental conditions, in contrast with corals whose sensitivity to eutrophication results in their absence from eutrophied settings. The well-known autoecology of foraminifera taxa can help to characterize environmental conditions of different habitats and regional environmental gradients. Although the use of fauna as bioindicators may be most robust when data are compared for multiple taxonomic groups, when such broad sampling is not available, benthic foraminifera are particularly well suited for environmental assessments due to their ubiquity, interspecific environmental breadth, and the well-understood environmental preference of individual taxa.