Toll and Toll-related proteins play an important role in antibacterial innate immunity in insect, plants, and mammals. We present the first comprehensive phylogenetic analyses of Toll-related genes from both insects and mammals. Drosophila melanogaster contains Toll and a highly homologous gene, Tehao. The protein, Dm Tehao, comprises 795 amino acid residues and its cytoplasmic domain shares a striking 61% identity with Dm Toll. Two Toll homologues were found in another dipteran of medical importance, Anopheles gambiae, a vector for human malaria. One Toll-like gene each was identified from Aedes aegypti and Glossina palpalis palpalis, vectors for yellow fever and trypanosomiasis, respectively. Phylogenetic analyses revealed separate clustering of Toll and related proteins from insects and mammals, suggesting independent evolution of the Toll family of proteins and of innate immunity in arthropods and vertebrates. These results also provide new avenues to understanding the function of Toll proteins in insect innate immunity against bacteria, fungi, and protozoans.