Molecular clock estimates of divergence times for artiodactyls and whales vary widely in their agreement with the fossil record. Recent estimates indicate that the divergence of whales from artiodactyls occurred 60 Ma, a date which compares well with the first appearances of fossil whales around 53.5 Ma, and artiodactyls at 55 Ma. Other estimates imply significant gaps in the fossil record. A date of 65 Ma for the divergence of Suidae and Ruminantia predates the appearance of Ruminantia by over 10 million years, and an estimate of 58 Ma for the divergence of Suidae from Cetacea implies a gap of over 20 million years. Further, although a molecular clock estimate has not been reported, the hypothesis that hippos are the closest living relatives of the whales implies a potential ghost lineage for hippos of over 40 million years. There are only two living species of hippos, and their fossil record is sparse, while cetaceans and other artiodactyls are speciose and have rich fossil records. A 40-million-year gap in the fossil record of hippos could be explained by several possibilities: inadequate biogeographic sampling, taphonomic biases, or undifferentiated primitive morphology. Similarly, a number of possible problems may exist in the molecular data: rate variation in the genes sampled, the low numbers of genes examined, and insufficient age calibrations. In addition, there are potential problems in molecular phylogeny estimation, such as long branch attraction and inappropriate taxonomic sampling. Additional estimates of divergence times among living taxa should provide a broader framework for comparison with the fossil record and provide information to help identify which of these factors are causing conflict.