Platynereis dumerilii is an emerging model system for both comparative developmental biology and ecotoxicology. As such it would be extremely valuable to be able to map the location of genes and markers in its genome, in order to understand how the genome changes or has changed, either due to chemical and environmental insults or during evolution. Here we report the adaptation of the technique of chromosomal fluorescence in situ hybridization (FISH) to P. dumerilii for the localization of single-copy genes. Also the duplicated ribosomal gene cluster of this annelid is more reliably revealed with FISH than with the previous technique of silver staining. This duplicated ribosomal cluster correlates with polymorphisms in the internal transcribed spacer (ITS) regions, which has implications for the use of these regions in phylogenetic or population biology work.