Chromoviruses, chromodomain-containing retrotransposons, are the only Metaviridae (Ty3/gypsy group of retrotransposons) clade with a Eukaryota-wide distribution. They have a common evolutionary origin and are the most prolific and diverse Metaviridae clade. The fusion of a retrotransposon and a chromodomain, was most probably responsible for their extreme evolutionary success in Eukaryota. Analysis of the massive amount of genome sequence data for different eukaryotic lineages has provided an in depth insight into the diversity, evolution, neofunctionalization, high rate of genomic turnover and origin of chromoviruses in Eukaryota. This review attempts to summarise the unique aspects of chromoviruses from a genomic perspective.