The Chromatin Organization Modifier Domain (chromodomain) is a protein domain of approximately 50 residues in length, originally identified as a motif common to the Drosophila chromatin proteins Polycomb (Pc) and the heterochromatin protein1 HP1. Chromodomains are involved in chromatin remodeling and regulation of the gene expression in eukaryotes (Koonin, Zhou and Lucchesi 1995; Cavalli and Paro 1998). Almost but not all elements belonging to a lineage of Metaviridae Ty3/Gypsy LTR retrotransposons described in the genomes of plants, fungi, and vertebrates, are carriers of a chromodomain displayed at the C-terminal end of their integrases (Malik and Eickbush 1999). In light of this evidence, the term "Chromoviridae" was suggested to describe this lineage as a genus (Marin and Lloréns 2000) whose diversity has been found to be greater than previously thought (Gorinsek, Gubensek and Kordis 2004; 2005). The origin of chromoviruses has been significantly extended by the finding of representatives in the most basal plant lineages, those of green and red algae (Gorinsek, Gubensek and Kordis 2004; 2005), revealing that within Ty3/Gypsy elements, chromoviruses represent the so far oldest and most widespread lineage (See also Kordis 2005).