We report on the isolation of dinucleotide microsatellites from the polychaete Pectinaria koreni using (GT)(10) and (CT)(10) olignonucleotide probes. Compound and particularly imperfect microsatellites are predominant in this species. In most cases the associated element is (AT)(n) leading to AT microsatellites being the most frequent class after GT repeats. Obtaining single-copy polymerase chain reaction products in the expected size range proved to be difficult, and only 24% of the primer pairs tested produced polymorphic single-locus markers. We obtained five highly variable loci with 16 to 41 alleles and an observed heterozygosity ranging from 0.29 to 0.81. Amplifications have also been obtained from the earliest postlarval stage. These highly informative markers will allow studies of the population structure of P. koreni at fine spatial and temporal scales.