As climate change，international trade，and human activities increasingly disrupt traditional geographic barriers in the oceans，non-indigenous species（NIS）have successfully established themselves outside their native ranges. Outbreaks of NIS can pose significant threats to local ecosystems and economies，making them a critical issue for marine biodiversity and biosecurity. Biological invasions in marine habitats differ significantly from those on land or in freshwater. Detection and identification of NIS in marine habitats is particularly challenging due to difficulties in sampling，morphological identification，and visualization in the early stages of outbreaks. Environmental DNA（eDNA）approaches have emerged as reliable and cost-effective methods for both qualitative and quantitative detection of marine NIS，particularly in the introductory phase. In this review，we summarize recent applications and advances in eDNA-based detection of marine NIS. We emphasize that innovations in eDNA sampling equipment，improvements in detection methods，and further refinement of the reference genomic database for marine species are crucial for the future development of this field.