In the past, molecular clocks have been used to estimate divergence times among animal phyla, but those time estimates have varied widely (1200–670 million years ago, Ma). In order to obtain time estimates that are more robust, we have analysed a larger number of genes for divergences among three well–represented animal phyla, and among plants, animals and fungi. The time estimate for the chordate–arthropod divergence, using 50 genes, is 993 ± 46 Ma. Nematodes were found to have diverged from the lineage leading to arthropods and chordates at 1177 ± 79 Ma. Phylogenetic analyses also show that a basal position of nematodes has strong support (p > 99%) and is not the result of rate biases. The three–way split (relationships unresolved) of plants, animals and fungi was estimated at 1576 ±88 Ma. By inference, the basal animal phyla (Porifera, Cnidaria, Ctenophora) diverged between about 1200 – 1500 Ma. This suggests that at least six animal phyla originated deep in the Precambrian, more than 400 million years earlier than their first appearance in the fossil record.