Retroelements are mobile DNA sequences very abundant in eukaryotic genomes, that include retrotransposons and retroviruses. All groups of retroelements differ greatly in their structure, but one thing the vast majority of them have in common is their RT domain which encodes reverse transcriptase, an enzyme involved in their transposition. Reverse transcriptase amino acid sequences and RT domain nucleotide sequences represent the main choice in conducting phylogenetic analyses of retroelements, but due to their high frequency of horizontal transfer and other factors affecting their evolution, these analyses are made difficult. Additional support can be provided by phylogenetic analyses based upon other domains that are common to some individual groups. In this regard, the phylogenetic relations of all groups of retroelements, together with certain groups of viruses and some eukaryotic and even bacterial enzymes, were determined, and the origin of retroviruses clarified. Retroelements integrated into genomes are subject to natural selection, and depending on their effect on their host’s viability and reproductive success, they can be lost or fixed in the population, thus affecting the evolution of their host’s genome.