Ports are urban and often quite-confined habitats within the aquatic (marine or freshwater) ecosystems, hosting biodiversity as any natural ecosystem under anthropogenic pressures as in many urban ecosystems. This scoping review seeks to give an overview of the state of knowledge on port biodiversity and port concerns about biodiversity based on scientific literature. Our aim was to highlight gaps and strengths in biodiversity knowledge and research in the port ecosystem, the outcomes of which are supposed to inform port authorities, guide port management and assist in planning research and management actions towards the implementation of relevant measures for port environmental sustainability. Results using Web of Science showed a recent trend in port biodiversity research (no references before 1999, most published after 2016) with a shift of research objective from empirical knowledge early-on towards non-indigenous species (NIS) concern recently. European, commercial ports and the NIS concern dominated the landscape. Fish, invertebrates such as crustaceans, major international and inland (freshwater) ports were under-represented. This review highlighted the need for a shift in port environmental awareness for biodiversity to expect resilience of the whole social-ecological system and for baseline knowledge and exhaustive inventories to assess how anthropogenic activities impact biodiversity and change ecosystem properties and functions.