Recent concerns over the status of wild gadoid populations together with the increasing cultivation of a number of gadoid species has prompted the search for new genetic markers, Minisatellite containing clones were isolated by screening a size selected whiting (Merlangius merlangus L.) genomic DNA library with Jeffrey's 33.15 and 33.6 probes. A partial sequence of one of these clones revealed a minisatellite repeat with a core sequence of 31bp. PCR primers complimentary to both sides of the minisatellite region were designed and following optimisation of PCR amplification conditions, either one or two products per individual were amplified with sizes ranging from 460 to 1870bp. Familial analysis has confirmed the Mendelian inheritance of the products. Screening of whiting populations from the Irish Sea (n=50), Baltic Sea (n=50), Atlantic coast of Norway (n=100), south North Sea (n=100) and north North Sea (n=50) revealed a minimum of 24 resolvable alleles per population with a mean heterozygosity value of 0.94. UPGMA cluster analysis based on Nei's genetic distance indicated that geographically adjacent populations were more similar. A similar highly variable region in cod (Gadus morhua L.) and haddock (Merlanogrammus aeglefinus L.) is also amplified using these primers.