This paper is the first attempt to resolve relationships among the Ceratocanthinae: Ceratocanthini pill scarab beetles using DNA sequences. It is focused on the Philharmostes group of seven Afrotropical genera: Baloghianestes (3 spp.), Callophilharmostes (1 sp.), Carinophilharmostes (1 sp.), Chaetophilharmostes (1 sp.), Cryptophilharmostes (3 spp.), Petrovitzostes (1 sp.) and Philharmostes (31 spp.). A phylogenetic analysis of 46 terminals and alignment of 2,913 bp from one mitochondrial and two nuclear fragments corroborates monophyly of this group, but rejects that of Philharmostes, the largest genus. The latter is paraphyletic with respect to at least four other smaller genera and consists of at least three distantly related clades. One of them, formed by Philharmostes ballerioi sp. n. from the Tanzanian Nguru (the type locality) and Kaguru Mountains, is sister to the rest of the entire Philharmostes group. The nominal genus Philharmostes is, therefore, a waste-basket taxon for accommodating members of this group that lack the distinct characters of the smaller genera. Pending further research, the phylogenetically inadequate generic taxonomy of the Philharmostes group is not modified. Molecular clock analysis estimates separation of the mitochondrial lineages of two known populations of the new species at about 2.2 Ma, which corresponds with recurring shrinkage and expansion of African rainforest caused by climatic fluctuations during the Pleistocene. Adults of all nominal ingroup genera are illustrated along with male and female body parts of the new species. Diagnostic and/or synapomorphic morphological characters of the Philharmostes group of genera are revised. Habitus images and other supplementary information on all sequenced specimens are available online at dx.doi.org/10.5883/DS-VGDS001 and dx.doi.org/10.5883/DS-VGDS004.