This study examined the evolutionary dynamics of Bov-B LINEs in vertebrates and the evolution of the RTE clade of non-LTR retrotransposons. The first full-length reptilian Bov-B LINE element is described; it is 3.2 kb in length, with a structural organization typical of the RTE clade of non-LTR retrotransposons. The long-term evolution of Bov-B LINEs was studied in 10 species of Squamata by analysis of a PCR-amplified 1.8-kb fragment encoding part of apurinic/apyrimidinic endonuclease, the intervening domain, and the palm/fingers subdomain of reverse transcriptase. A very high level of conservation in Squamata Bov-B long interspersed nuclear elements has been found, reaching 86% identity in the nearly 600 amino acids of ORF2. The same level of conservation exists between the ancestral snake lineage and Ruminantia. Such a high level is exceptional when compared with the level of conservation observed in nuclear and mitochondrial proteins and in other transposable elements. The RTE clade has been found to be much more widely distributed than previously thought, and novel representatives have been discovered in plants, brown algae, annelids, crustaceans, mollusks, echinoderms, and teleost fishes. Evolutionary relationships in the RTE clade were deduced at the amino acid level from three separate regions of ORF2. By using different independent methods, including the divergence-versus-age analysis, several examples of horizontal transfer in the RTE clade were recognized, with important implications for the existence of HT in non-LTR retrotransposons.