Quantifying the broad-scale distribution and abundance of non-indigenous species (NIS) is necessary to provide accurate estimations on impacts of invasions, to prioritize research, and to guide national management. Sediment grab-sampling is a standardized method for monitoring marine benthos. In Denmark, ~45,000 grab-samples were collected from 1970 to 2005. Using these samples, we compared densities of NIS and native species among 27 broad spatio-temporal groupings. Eight known NIS and one ‘cryptogenic species’ (the polychaete Neanthes succinea) were found in the samples. Most were present in low abundance, but the bivalve Mya arenaria, likely introduced by the vikings from North America, was particularly abundant. M. arenaria was found in ca. 20% of all samples and was among the 10 most common species in all of Denmark. M. arenaria’s high abundance, high filtration capacity and importance in food-web interactions, suggest that this species has dramatically impacted shallow coastal ecosystems in Denmark. The polychaete Marenzelleria viridis, the gastropod Potamopyrgus antipodarum and N. succinea were also widespread and abundant, and they too are likely to have had broad-scale impacts. In conclusion, 28% of grab-samples collected in Denmark over 35 years were affected by some degree of NIS or cryptogenic species, suggesting that centuries of human-mediated transfer of organisms has had a profound impact on the ecology of soft-bottom systems in Denmark.