A total of 7806 nucleotide positions derived from one mitochondrial and eight nuclear DNA segments were used to provide a robust phylogeny for members of the order Artiodactyla. Twenty-four artiodactyl and two cetacean species were included and the horse, order Perissodactyla, was used as the outgroup. Limited rate heterogeneity was observed among the nuclear genes. The partition homogeneity tests indicated no conflicting signal among the nuclear gene fragments and the sequence data were analyzed together and as separate loci. Analyses based on the individual nuclear DNA fragments, and 34 unique indels, all produced phylogenies largely congruent with the topology from the combined data set. In sharp contrast to the nuclear DNA data, the mtDNA cytochrome b sequence data showed high levels of homoplasy, failed to produce a robust phylogeny, and were remarkably sensitive to taxon sampling. The nuclear DNA data clearly support the paraphyletic nature of the Artiodactyla. Additionally, the family Suidae is diphyletic and the non-ruminating pigs and peccaries (Suiformes) were the most basal cetartiodactyl group. The morphologically derived Ruminantia was always monophyletic and within this group all taxa with paired bony structures on their skulls clustered together. The nuclear DNA data suggested that the Antilocaprinae comprise a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa while the Giraffidae is more primitive.