Two molecular methods, mitochondrial and intron DNA markers, were used to determine genetic relationships among Antarctic toothfish (Dissostichus mawsoni) samples from three CCAMLR areas: Subareas 48.1 and 88.1 and Division 58.4.2. D. mawsoni appeared to be characterised by low diversity; no genetic variation was detected with restriction enzyme digests of nine sub-regions of the mitochondrial genome. Polymorphisms were found in four of seven introns digested with the restriction enzymes, but there was no population differentiation among the three sea areas. Direct sequencing of cytochrome b (665 bp) and the left domain of the control region (639 bp) showed very little variation and no significant genetic differentiation among sea areas.