Abstract The mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are a speciose and ubiquitous group of sap-sucking plant parasites, many of which are very serious agricultural pests. There has been much work on the alpha-level taxonomy, amounting to the description of more than 2000 species, but suprageneric relationships remain poorly known. Downie & Gullan reviewed proposed schemes for a mealybug subfamily-level classification and used DNA sequence data from three nuclear genes to infer the mealybug phylogeny. They recognized three subfamilies: the Rhizoecinae, the Phenacoccinae, and the Pseudococcinae; and within the Pseudococcinae, recognized the tribes Pseudococcini, Trabutinini, and Planococcini. Excepting the Trabutinini, none of these groupings was well-supported. We improve our estimation of the mealybug phylogeny by: (i) increasing the taxon sampling by 50%; (ii) adding a morphological character matrix; and (iii) performing mixed model Bayesian and maximum likelihood inference procedures. We recover two primary clades within the Pseudococcidae, to which we apply the subfamily names Phenacoccinae and Pseudococcinae. Within the Phenacoccinae, we recover support for the monophyly of the hypogaeic mealybugs (Rhizoecini), and within the Pseudococcinae, we find support for the tribes Pseudococcini, Trabutinini, and Planococcini. Our results suggest a clear sequence of (i) β-Proteobacteria primary endosymbionts infecting the mycetome of the most recent common ancestor of the Pseudococcinae, followed by (ii) γ-Proteobacteria secondary endosymbionts infecting the primary β-Proteobacteria endosymbionts. For each subfamily, we provide a morphological diagnosis and a comprehensive list of included genera. We resurrect the genus Ceroputo Šulc, currently under synonymy with the genus Puto Signoret (Putoidae), and place it in the mealybug subfamily Phenacoccinae. Greenoripersia kaiseri Bodenheimer is transferred from the Pseudococcidae to the Eriococcidae.