Despite many years of effort, the relationships within and between major groups of metazoa remain uncertain and controversial. Using substantial quantities of sequence data from several key animal taxa, Rokas et al. (p. 1933; see the Perspective by Jermiin et al.) find a contrast between the history of the metazoan and fungal kingdoms—two groups that originated at a similar time in life's history. In particular, for animals, the lack of resolution of ancient clades is a signature of closely spaced series of clade-generating events. This explicit molecular support for the rapid radiation of animals is in agreement with previous inferences from the fossil record.