During the last 200 years, the riparian ecosystem along major rivers has been reduced to a few scattered remnants. Important elements of the riparian ecosystem are water bodies which were originally connected to the main river channel by annual floodings. Due to river regulations many of these remnants are now virtually isolated. In an allozyme analysis using roach, Rutilus rutilus, as a study species we demonstrate that the genetic diversity (number of alleles per locus, expected heterozygosity) of populations living within floodplain water bodies is not severely impoverished compared to the genetic diversity within the main river channel. However, we found slight differences in the allele frequencies of flood plain water bodies and the main river channel. Nevertheless, fish populations in floodplain water bodies may serve as reservoirs of autochthonous genetic material for restoration of fish populations in the main river channel after population extinction due to catastrophic accidents (e.g. industrial pollution).