Antarctic plunderfishes (Notothenioidei, Artedidraconidae) are important components of the Southern Ocean fish fauna. As a contribution to the Victoria Land Transect Project, we performed a cytogenetic analysis of six species from three of the four artedidraconid genera, Artedidraco glareobarbatus, A. orianae, A. skottsbergi, A. shackletoni, Histiodraco velifer, and Pogonophryne sp. We investigated the species-specific cytogenetic features and highlighted patterns of chromosomal evolutionary change using a molecular phylogeny based on mitochondrial and nuclear genes. Despite a conserved diploid number, some important karyotypic traits account for major differences among artedidraconid species. Specific cytogenetic features, including the chromosomal organization of ribosomal genes and the occurrence of sex chromosomes, are characteristics of A. skottsbergi, making this species distinct among those studied. These chromosomal peculiarities are consistent with the phylogenetic hypothesis resolving A. skottsbergi as the sister lineage of all other Artedidraconidae. A karyological similarity was found between A. glareobarbatus and A. shackletoni consistent with their inferred sister species relationship in the phylogeny. The results indicate that artedidraconids are not conservative in their genomic organization at the chromosomal level and provide new evidence for the degree of biological diversity in this notothenioid group.