Artedidraconids (Plunderfishes) are small benthic notothenioid fishes of the Antarctic and South Georgia shelf and slope. The family Artedidraconidae is monophyletic; however, the relationships within the family have remained poorly explored until now, and based on a small sample of the genus Artedidraco. The present study focuses on the interrelationships among the artedidraconid genera and the phylogeny of the genus Artedidraco. 2,353 base pairs from 77 specimens were sequenced from the partial mitochondrial cytochrome oxidase I gene and cytochrome b gene, the partial mitochondrial control region and the partial nuclear rhodopsin retrogene. The genus Artedidraco is not monophyletic, confirming the preliminary relationships found by Derome et al. (Mol Phylogenet Evol 24:139–152, 2002): Pogonophryne, Dolloidraco and Histiodraco are well embedded within the genus Artedidraco. From Artedidraco skottsbergi and A. loennbergi to A. orianae and A. mirus, the tree shows that there is an increasing number of upper lateral line tubular scales and decreasing number of disc-shaped scales. There is also a trend toward a decrease in the number of epipleural ribs and an increase in number of pleural ribs along the tree.