Polintons are a recently discovered group of large transposable elements (<40 Kb in size) encoding up to 10 different proteins. The increasing number of genome sequencing projects has led to the discovery of these elements in genomes of protists, fungi, and animals, but not in plants. The RepBase database of eukaryotic repetitive elements currently contains consensus sequences and information of 70 Polinton elements from 28 organisms. Previous phylogenetic analyses have shown the relationship of Polintons to linear plasmids, bacteriophages, and retroviruses. However, a comprehensive phylogenetic analysis of all known Polintons has been lacking. We retrieved the Polinton consensus sequences from the most recent version of RepBase, and compiled amino acid sequences for the two most common Polinton-specific genes, the DNA polymerase-B and retroviral-like integrase. Open reading frame predictions and homology comparisons revealed partial or full sequences for 54 polymerases and 55 Polinton integrases. Multiple sequence alignments portrayed conservation in several functional motifs of these proteins. Phylogenetic analyses based on Bayesian inference using single- and combined-gene datasets revealed seven distinct lineages of Polintons that broadly follow the tree of life. Two of the seven lineages are found within the same species, indicating that ancient divergences have been retained to this day. (C) 2014 Elsevier Inc. All rights reserved.