Anonymous nuclear DNA polymorphisms were developed for the marine mussel Mytilus by cloning tandem segments of nuclear DNA, sequencing the ends, constructing primers to amplify the cloned segments, and restricting the PCR product. The technique of PCR RFLP analysis was applied, for three cloned segments, using genomic DNA preparations from the three closely related mussel species, Mytilus edulis L., Mytilus galloprovincialis (Lamarck) and Mytilus trossulus (Gould) sampled from European populations. M. trossulus was found to differ at the nucleotide level from the other two species which were closely similar. This result contrasts with that obtained for mtDNA where M. edulis and M. trossulus have higher resemblance, and for allozymes where genetic distance values between the species are similar. The contrasting results for mtDNA and nuclear polymorphisms can be attributed to extensive mtDNA gene flow between M. edulis and M. trossulus.