Toll-like receptors (TLRs) are an important part of the innate immunity system and are found throughout the animal kingdom, but have not yet been reported in annelids. We searched shotgun reads of the genomes of the leech Helobdella and polychaete Capitella for TLR homologs. We found 105 TLR homologs in Capitella and 16 in Helobdella. The deduced phylogeny of these sequences, together with TLRs from other animal phyla, reveals three major clades. One clade consists of a mixture of both vertebrates and invertebrates, including sequences from Capitella and Helobdella, while the other two clades contain only invertebrate TLRs.