Coccoidea (scale insects) are important plant parasites with high diversity of species. However, the phylogenetic relationship within Coccoidea has not been fully determined. In this study, we sequenced mitogenomes of six species belonging to five coccoid families. With the addition of three previously published mitogenomes, a total of 12 coccoid species were adopted for the phylogenetic reconstruction based on the maximum likelihood and Bayesian inference. The monophyly of Coccoidea was recovered and Aclerdidae and Coccidae were recovered as the sister group, successively sister to Cerococcidae, Kerriidae, and Eriococcidae. In addition, there were gene rearrangements occurring in all mitogenomes of coccoid species studied here. The novel gene rearrangement ND6-trnP and trnI-ND2-trnY supported the monophyly of Coccoidea and the sister relationship of Aclerdidae and Coccidae. This implies that data from the mitogenome can provide new insight for clarifying the deeper level of phylogenetic relationship within Coccoidea.