Ceratovacuna and Pseudoregma are important groups in Cerataphidini (Hemiptera, Hormaphidinae) that not only produce soldier aphids in galls on the primary hosts but also produce horned soldiers on the herbaceous secondary hosts. However, due to sampling bias in previous studies, the phylogenetic relationships of these two genera remain inconclusive. In this study, based on more extensive sampling and examination of both mitochondrial (cytochrome c oxidase subunit I (COI); cytochrome b (Cytb)) and nuclear (elongation factor-1α (EF-1α); long-wavelength opsin (LWO)) genes, we reconstructed the phylogenetic relationships of Ceratovacuna and Pseudoregma. Phylogenetic analyses, along with morphological evidence, suggested that these two genera belong to the paraphyletic groups with species clustered into three main groups. The monophyly of Ceratovacuna and Pseudoregma as a whole was generally supported by all analyses. Monophyly of Pseudoregma was also supported. The estimated divergence times demonstrated that diversification of Ceratovacuna and Pseudoregma occurred approximately at 10 mya. The relatively low resolution for the basal relationships of the three main clades may indicate that these two genera have experienced a rapid radiation along with speciation burst of their secondary hosts during the late Tertiary.