The soft scales (Hemiptera: Coccidae) are plant-sucking insects, some of which are considered as serious agricultural pests. Here, we performed phylogenetic analysis of Coccidae, based on molecular fragments 1813bp containing mitochondrial DNA (COI), nuclear ribosomal RNA genes (18S and 28S), and elongation factor 1α (EF1-α). Data sets of 64 taxa were analyzed using maximum likelihood (ML) and Bayesian inference (BI). Our molecular analyses represent: 1) Monophyletic clade of Ceroplastinae is nested within the major clade of Coccinae; 2) Four tribes of Coccinae are paraphyletic, especially Megapulvinaria and Paralecanium not clustered within the major clade of Coccinae; 3) Didesmococcus is separated from the clade of Eulecaniinae; 4) Filippiinae and Cardiococcinae are paraphyletic with respect to some of Coccinae and Eulecaniinae.