The phylogenetic study of the deep-sea genus Bentheogennema is based on four molecular markers and 79 morphological characters. All four previously recognized species and two new species of Bentheogennema, representatives of all other genera and species groups of Benthesicymidae, and three outgroups were included in the analyses. We have examined and coded six major groups of morphological characters related to the carapace (three characters), the pleon and the telson (14), the mouthparts (nine), the armature of the pereopods (five), the thelycum (27) and the petasma (21). Results of morphological and molecular analyses were similar. Two species were transferred from Bentheogennema to other genera (for one of them a new genus was erected) and two new species of Bentheogennema were described. Three pelagic genera (Gennadas, Bentheogennema and a new genus) created a robust clade. The divergence of this clade is linked to 'smoothening' of the body (reduction of the branchiostegal spine on the carapace, reduction and loss of the dorsolateral spines and the end-piece on the telson) and elaboration of the copulatory structures. We provide amended diagnoses of these three pelagic genera and key to species of Bentheogennema.