A recent total evidence analysis of the position of cetaceans (whales, dolphins and porpoises and extinct relatives) among mammals indicated that the phylogeny of these taxa remains poorly resolved. Molecular data show that 1) the order Artiodactyla (even-toed ungulates) is paraphyletic unless whales are included within it and 2) that the traditional relationships of clades within Artiodactyla are not supported. This controversy also affects the position of a wholly extinct clade, Mesonychia, which has been argued to be the group of terrestrial mammals most closely related to whales. Here I update a previous total evidence analysis by adding several hundred new informative molecular characters from the literature. Even with the addition of these characters the phylogeny remains unresolved. All most parsimonious trees, however, indicate a paraphyletic Artiodactyla with conflict existing over the exact sister taxon of Cetacea. Congruence between different equally parsimonious cladograms and the stratigraphic record as measured using the modified Manhattan Stratigraphic Measure shows that all of the competing topologies, including those with a paraphyletic Artiodactyla, are significantly congruent with the stratigraphic record. In fossil taxa cladistic optimization can be used as an alternative to “argument from design” (Lauder, 1996) to reconstruct behavior and soft tissues that do not fossilize or osteological characters that have not preserved. In certain scenarios of cetacean phylogeny, optimization indicates that taxa such as the archaic whales Ambulocetus and Pakicetus, and possibly mesonychians, are more correctly reconstructed without hair.