It is demonstrated here that Charcotia Chevreux, 1906 (Amphipoda) has priority over Charcotia Vayssière, 1906 (Gastropoda), and that Waldeckia Chevreux, 1906 has to be treated as an invalid objective junior synonym of Charcotia Chevreux, 1906. An analysis of a part of the mitochondrial COI gene of Charcotia indicates that Charcotia obesa sensu lato, consists of two genetically distant clades that fulfil the criteria of genetic species. Each genetic clade corresponds to a different morphotype. The first one has a low triangular protrusion on the dorsal border of urosomite 1, a strong tooth on epimeron 3, and the posterodistal corner of the basis of pereiopod 7 is regularly rounded. It agrees with the original description of Charcotia obesa Chevreux, 1906. The second one has a protrusion of urosomite 1 prolongated by a sharp and usually long denticle, a small tooth on epimeron 3, and the posterodistal corner of the basis of pereiopod 7 is bluntly angular. The second form is treated herein as a new species, Charcotia amundseni sp. nov., which is described in detail. While the bathymetric distribution of the two Antarctic Charcotia species overlaps (0–300 m for C. obesa and 7–1200 m for C. amundseni sp. nov.), C. obesa largely predominates at depths of less than 150 m, while Charcotia amundseni sp. nov. predominates at greater depths. Both species are widely distributed and presumably circum-Antarctic.