Coccidae is one of the major families of scale insects, with many species considered to be serious agricultural or horticultural pests. However, the phylogenetic relationships among coccid subfamilies, tribes and genera are poorly understood because the previous hypotheses are based only on morphological characters and cladistic analysis. Here, we present the first molecular phylogeny of the family based on DNA fragments of a mitochondrial gene (COI), nuclear ribosomal RNA genes (18S and 28S), and elongation factor-1α (EF-1α). We recover a monophyletic family Coccidae with strong support. However, some genera (Coccus and Pulvinaria), tribes (Coccini, Paralecaniini, Pulvinariini and Saissetiini) and subfamilies (Coccinae and Filippiinae) within the family found to be paraphyletic- or polyphyletic. Moreover, particular types of wax formation, which have been used as important taxonomic characters in Coccidae, were found in several unrelated taxa.