The transition in the cetaceans from terrestrial life to a fully aquatic existence is one of the most enduring evolutionary mysteries. Resolving the phylogenetic relationships between Cetacea and the other orders of eutherian mammals may provide us with important clues to the origin of whales and may help us date the evolutionary transition to aquatic life. Previous paleontological and molecular evidence has indicated that cetaceans and artiodactyls constitute a natural clade within subclass Eutheria. Our present phylogenetic analyses of protein and mitochondrial DNA sequence data indicate that cetaceans are not only intimately related to the artiodactyls; they are in fact deeply nested within the artiodactyl phylogenetic tree; i.e., they are more closely related to the members of one suborder of artiodactyls, the Ruminantia, than either ruminants or cetaceans are to members of the other two artiodactyl suborders: Suiformes and Tylopoda. On the basis of the rate of evolution of mitochondrial DNA sequences and using paleontological reference dates for calibration, we estimate that the whale lineage has branched off a protoruminant lineage < 50 Mya. By implication, the cetacean transition to aquatic life is inferred to be a relatively recent evolutionary event.