The first lentivirus isolated from sheep in Brazil was analysed phylogenetically. Evolutionary trees of the proviral 597 nucleotide gag and 432 nucleotide pol sequences obtained by the maximum likelihood method demonstrated that the sheep isolate clustered with prototype Maedi Visna virus whereas three lentiviruses isolated from goats in the same geographic region were close to caprine arthritis encephalitis prototypes. A subsequent comparison of sequence data of these viruses with those contained in the EMBL sequence database revealed that, in contrast to caprine prototypic viruses, all prototypic Maedi Visna viruses contain a deletion of six nucleotides in the gag gene resulting in the deletion of two residues in the central region of capsid protein. This deletion may be a useful marker in the analysis of small ruminant lentiviruses, especially when considering possible transmission of lentiviruses between sheep and goats.