The genus Carinina Hubrecht, 1885 has long been considered the most ‘archaic’ nemertean taxon because its members are distinguished by the basiepidermal position of the brain and lateral nerve cords, characters thought to be plesiomorphic for the phylum. Here we describe two new species, Carinina yushini sp. nov. from the Sea of Japan (Russia) and C. chocolata sp. nov. from the north-east Pacific (Oregon, USA), distinguished by brown body colour. A phylogenetic analysis based on partial sequences of five nuclear and mitochondrial gene regions, 18S rRNA, 28S rRNA, histone H3, 16S rRNA and COI, confirms the monophyly of Carinina (Family Carininidae), and points to a close relationship to Carinoma (Family Carinomidae). The two groups together form a sister clade to the rest of the palaeonemerteans (Family Tubulanidae + Family Cephalotrichidae s.l.). Carinina plecta most likely belongs to the Tubulanidae. A morphological synapomorphy of the clade Carininidae + Carinomidae is a larva with a single midventral eye (in contrast to eyeless larvae of the Tubulanidae and two-eyed larvae of the Cephalotrichidae). Our phylogenetic analysis suggests that the basiepidermal position of the central nervous system is an autapomorphy of Carininidae (and, independently, C. plecta), rather than a plesiomorphy of the phylum Nemertea or the class Palaeonemertea, emphasising that the genus Carinina is no more archaic than any other palaeonemertean genus.