The nucleic acid sequences of three geminiviruses with bipartite genomes and of two viruses having a single genome component were analyzed and phylogenetic relationships deduced. Sequences in coding and noncoding regions were considered at the nucleotide and amino acid levels by several methods. The results suggested that the viruses are phylogenetically related to different degrees. All the viruses contain in an intergenic region a consensus sequence (TAATATTAC) that is postulated to be required for a critical virus function, such as replication and/or transcription. Estimates of divergence in one putative gene that all of the viruses share were used to construct a phylogenetic tree. Among the bipartite-genome viruses, bean golden mosaic virus and tomato golden mosaic virus are more closely related than either is to cassava latent virus. The single-component viruses (maize streak and wheat dwarf viruses) and one of the two DNA components of the other three viruses were postulated to be distant relatives descended from a common ancestral sequence.