The notothenid species Trematomus bernacchii has previously been shown, by allozyme analysis, to be a complex of two cryptic species, one of which being more closely related to T. hansoni than to the other T. bernacchii cryptic species. Two T. bernacchii colour morphs, “white blotch” and “brown”, at McMurdo Sound, may correspond to these cryptic species. In this study, we present mitochondrial DNA sequences of the 12S and 16S ribosomal regions for six “white blotch” morphs, eight “brown” morphs collected in McMurdo Sound, one individual collected off the Antarctic Peninsula, and two T. hansoni individuals from McMurdo Sound. These sequences were compared with those of T. bernacchii and T. hansoni in the literature. Based on 14 phylogenetically informative sequences, no differences were found between “white blotch” and “brown” morphs. Furthermore, only one substitution separated these sequences from the previously published T. hansoni sequence, while 10 substitutions separated them from the previously published T. bernacchii sequence. Misidentified specimens, and sequence misreadings may be at the origin of these discrepancies. However, the presence of cryptic species within T. bernacchii and T. hansoni is not ruled out.