Acquired Immune Deficiency Syndrome (AIDS) is caused by two different Human Immunodeficiency Viruses, HIV-1 and HIV-2. Closely related viruses (SIVs) are found in many species of non-human primates. Phylogenetic analyses indicate that cross-species transmission events have been quite frequent. Both HIV-1 and HIV-2 appear to have resulted from multiple transfers of lentiviruses naturally infecting other primates; the source of HIV-2 appears to have been sooty mangabeys, whereas for HIV-1 the source may have been chimpanzees. Phylogenetic analyses also provide evidence that recombination has occurred between divergent viruses in vivo. Evolutionary trees based on various regions of the viral genome generally have consistent branching orders. However, some isolates fall into significantly different phylogenetic positions, indicating that their genomes are mosaics of sequences with different evolutionary histories. This implies that co-infection with highly divergent viral strains can occur in HIV-infected humans and SIV-infected primates; this could lead to the generation of hybrid genomes with significantly altered biological properties, and also has important implications for HIV vaccine development programmes.