In the context of increasing biological invasions, we investigated the invasion of the non-native polychaete Marenzelleria viridis in a shallow Danish estuary, Odense Fjord. Three datasets with different spatial and temporal resolution were examined to describe the invasion of M. viridis and to investigate its effect on the native benthic community with focus on the two common polychaetes, Nereis (Hediste) diversicolor and Arenicola marina. M. viridis colonized Odense Fjord rapidly and within 3 years it had spread to about 50% of the estuary. The population development of M. viridis in Odense Fjord followed the “boom-bust” pattern that is typical for many invaders. It is now firmly established and has reached an overall abundance of 100-200 individuals m-2 with local maxima of up to 1200 individuals m-2. The distribution of M. viridis is apparently regulated by abiotic parameters which prevent its establishment in the oligohaline and more silty parts of Odense Fjord. There was a positive interaction between M. viridis and the native A. marina. Otherwise the introduction of M. viridis was synchronous with a decrease of several macroinvertebrates species, especially N. diversicolor. The latter is still the dominant species in Odense Fjord, but its density has decreased by more than 60% in areas colonised by M. viridis. We do not expect that N. diversicolor disappears completely in this estuary, but it will probably be displaced to refuge areas where M. viridis cannot survive. Decrease in the population size of a key native species such as N. diversicolor might have significant ecological implications at the ecosystem level with respect to biodiversity and nutrient cycling.