Relatively few retroviruses have been characterised in vertebrates other than mammals and birds, limiting our understanding of their diversity and early evolution. Now, a recent study performed a phylogenomic analysis of endogenous retroviruses (ERVs) — which provide insights into past retroviral infections — in the genomes of 72 fish, 4 amphibians and 16 reptiles. ERVs were found to be ubiquitous in the genomes of jawed vertebrates. The authors identified >8,000 ERVs and reconstructed ~450 complete or draft ERV genomes. Their analyses revealed that these ERVs clustered into five major clades that have different host distributions and that most retroviruses frequently underwent host switching and many water–land transitions. The authors posit that their analyses reveal an ancient aquatic origin of retroviruses.