The evolution of the Metazoa from protozoans is one of the major milestones in life's history. The genetic and developmental events involved in this evolutionary transition are unknown but may have involved the evolution of genes required for signaling and gene regulation in metazoans. The genome of animal ancestors may be reconstructed by identification of animal genes that are shared with related eukaryotes, particularly those that share a more recent ancestry and cell biology with animals. The choanoflagellates have long been suspected to be closer relatives of animals than are fungi, the closest outgroup of animals for which comparative genomic information is available. Phylogenetic analyses of choanoflagellate and animal relationships based on small subunit rDNA sequence, however, have yielded ambiguous and conflicting results. We find that analyses of four conserved proteins from a unicellular choanoflagellate, Monosiga brevicollis, provide robust support for a close relationship between choanoflagellates and Metazoa, suggesting that comparison of the complement of expressed genes from choanoflagellates and animals may be informative concerning the early evolution of metazoan genomes. We have discovered in M. brevicollis the first receptor tyrosine kinase (RTK), to our knowledge, identified outside of the Metazoa, MBRTK1. The architecture of MBRTK1, which includes multiple extracellular ligand-binding domains, resembles that of RTKs in sponges and humans and suggests the ability to receive and transduce signals. Thus, choanoflagellates express genes involved in animal development that are not found in other eukaryotes and that may be linked to the origin of the Metazoa.