Diapausing egg banks of aquatic zooplankton have the potential to remain viable for decades or even centuries, and can thus harbour potentially high levels of genetic variation. Diapausing (ephippial) eggs from the Daphnia galeata–hyalina complex (Crustacea: Anomopoda) in Lake Constance (Bodensee), Germany, were isolated from sections of dated sediment cores, hatched in the laboratory, and established as a clone bank. We used cellulose acetate electrophoresis at four polymorphic enzyme loci (Pgm, Pgi, Ao, and Got) to examine long–term temporal changes in the genetic composition of the hatchling pool. Our results indicate that significant shifts have occurred in the genetic structure of this population, which parallel concomitant shifts in the trophic state of Lake Constance during the past 25–35 years. Here we discuss the utility of egg bank propagules as good model organisms to study microevolution, as related to past environmental change.