Peptidoglycan (PGN) recognition proteins (PGRPs) and gram-negative bacteria binding proteins (GNBPs) play an essential role in Toll/Imd signaling pathways in arthropods. The existence of homologous pathways involving PGRPs and GNBPs in other major invertebrate phyla such as the Mollusca remains unclear. In this paper, we report four full-length PGRP cDNAs and one full-length GNBP cDNA cloned from the snail Biomphalaria glabrata, the intermediate host of the human blood fluke Schistosoma mansoni, designated as BgPGRPs and BgGNBP, respectively. Three transcripts are generated from a long form PGRP gene (BgPGRP-LA) by alternative splicing and one from a short form PGRP gene (BgPGRP-SA). BgGNBP encodes a putative secreted protein. Northern blots demonstrated that expression of BgPGRP-SA and BgGNBP was down-regulated in B. glabrata at 6 h after exposure to three types of microbes. No significant changes in expression were observed in snails at 2 days post-exposure (dpe) to the trematodes Echinostoma paraensei or S. mansoni. However, up-regulation of BgPGRP-SA in M line snails at later time points of infection with E. paraensei (i.e., 12 and 17 dpe) was observed. Our study revealed that exposure to either microbes or trematodes did not alter the expression levels of BgPGRP-LAs, which were consistently low. This study provides new insights into the potential pathogen recognition capabilities of molluscs, indicates that further studies of the Toll/Imd pathways in this phylum are in order, and provides additional ways to judge the importance of this pathway in the evolution of internal defense across the animal phyla.