Acanthaspid isopods are well known from the deep sea regions of all oceans. Many species have been found also on the continental shelf around Antarctica. Phylogenetic relationships within the Acanthaspidiidae and the genetic differentiation of populations are poorly understood. In this study we analysed 16S rRNA gene sequences of 36 specimens of Acanthaspidiidae, including 17 specimens of Acanthaspidia drygalskii Vanhöffen, 1914. This species is known from several locations along the Antarctic shelf, supporting the idea of a circum-Antarctic distribution of this taxon. Our molecular data support the monophyly of all six species analysed, but there is only limited evidence for the interspecific relationships between the species. However, we were able to identify three distinct groups of haplotypes within Acanthaspidia drygaskii. Our results indicate the evidence of cryptic, reproductively isolated species. Further data are needed to understand mechanisms underlying speciation in deep sea isopods.