We used a combined morphological and genetic approach for species delineation within desmosomatid isopods in the eastern South Atlantic. Based on morphological data from light, scanning electron, and confocal laser scanning, microscopy as well as on mitochondrial (COI, 16S) and nuclear (18S) DNA markers, we describe two new species and a new genus. Chelator aequabilis is reported from the Guinea Basin and the Angola Basin. High intraspecific genetic variability did not allow final conclusions about relationships and species status of all analysed individuals. Due to the patterns of genetic variation and the subtle variation in some morphological characters, we conclude that more than one species might be hidden in C. aequabilis north of the Walvis Ridge. Chelator rugosus is described from the Cape Basin; the new monotypic genus Parvochelus is erected with the description of P. russus from the Guinea and the Brazil Basins. In Parvochelus, pereopod I bears a carpo-chela, especially the carpus is slender and long, its width is smaller than the merus width. The slender and long seta that is situated laterally to the carpo-propodal articulation is another characteristic feature. Despite the divergence within this species, shared lineages on both sides of the Mid-Atlantic Ridge suggest sporadic connectivity between populations on both sides. Our results document how molecular data can complement morphology in an integrative taxonomic approach elucidating biodiversity in the deep sea. Keys to the genera of Desmosomatidae and the species of Chelator are provided.