This study presents data on the DNA analysis of recent (2011–2013) samplings of Antarctic toothfish (Dissostichus mawsoni) from CCAMLR Subarea 48.5 (2013) and SSRUs 486G (2011), 5841E and 5841FG (2011), 5842E (2011), 881C (2011), 882A (2011, 2012) and 883C (2012). No significant genetic differences between geographic locations, or between samples collected in consecutive years, were observed. These results, based on analysis of the most informative subset of nuclear genetic markers of SNP variation presented in Kuhn and Gaffney (2008), do not support genetic differentiation of samples from the Ross Sea. Discrepancies in the allelic frequencies for several loci compared to previously published data highlight the need for further study of the genetics of Antarctic toothfish.