It has been proposed that anthropogenic eutrophication of lakes facilitated the establishment of populations of the cladoceran Daphnia galeata into the originally oligotrophic lakes north of the European Alps in the 1960s. This hypothesis lacks the support of studies on unproductive lakes, in which the past eutrophication is assumed to have never been on the level necessary for D. galeata to reach high abundances and to establish permanently. In order to investigate if such species shifts also happened in unproductive systems, we studied the past and present taxonomic composition of three ultra-oligotrophic Swiss lakes that were only marginally affected by eutrophication using molecular methods on diapausing eggs sampled from sediment cores. D. galeata temporarily established in unproductive lakes, but its colonization success seemed to depend on the general trophic state of the lake and the magnitude of eutrophication. In two of the studied lakes, D. galeata could establish a significant population size, whereas it was not successful in the most unproductive lake with the weakest eutrophication. Even in unproductive lakes, eutrophication led to partly irreversible species changes, providing evidence that this anthropogenic disturbance is responsible for species shifts in many pre-alpine lakes in Central Europe.