Twelve polymorphic dinucelotide microsatellites in the freshwater eel Anguilla anguilla L. were isolated and characterized. Genetic diversity was assessed in eels from Lake Constance, Germany. Allele numbers ranged from five to 26 per locus with observed heterozygosities between 0.125 and 0.875. A portion of locus AangCT77 aligns with a transcribed region of the zebrafish gene crystallin beta B2. Cross-species amplification of most markers was possible for nine other Anguilla eel species. The newly developed primer pairs will facilitate population and conservation genetic studies in order to refine the understanding of the subtle population genetic structure typical of eels, and to identify interspecies admixture due to global trade.