In lecanoid Coccids, or mealybugs, the male development is accompanied by the facultative heterochromatization of the entire, paternally derived, haploid chromosome set. This epigenetic phenomenon occurs in all the cells of mid-cleavage male embryos. Consequently, the Coccid chromosome system offers a powerful tool for gaining insights into the structure of facultative heterochromatin, and into the epigenetic mechanisms of its imprinted, developmentally regulated formation. This paper will present new data and summarize recent studies on genomic imprinting and facultative heterochromatization in mealybugs. First, the existence and the possible role of DNA methylation as an epigenetic modification that fulfills the requisites of the imprinting process in mealybugs will be considered. The second part of this paper will focus on proteins involved in the facultative heterochromatization process. In particular, the involvement of an HP-1-like protein in the silencing of the paternally derived haploid chromosome set and its interaction with the lysine 9 methylated isoform of histone H3 will be discussed.