Peptidoglycan recognition protein (PGRP) is considered an essential molecule for effective immunity in invertebrates by its detection and clarification of invading bacteria. Bivalve mollusks also possess PGRP systems for self-defense, however, their functions in bivalves remain to be understood. In the present study, cDNA of a novel PGRP was identified from the Pacific oyster, Crassostrea gigas, using EST-based RACE PCR. This novel PGRP is homologous to short PGRPs and the presence of a signal peptide was predicted. The PGRP is classified into the short PGRP group, although its molecular weight was estimated as 54 kDa, close to that of long PGRP groups. A conserved domain search detected amidase_2/PGRP and goose-type (g-type) lysozyme domains in this PGRP structure, and thus this novel PGRP was designated as CgPGRP-L. Catalytic residues for PGRP and g-type lysozyme are well conserved, suggesting that CgPGRP-L may have both binding and lytic functions against bacteria. Reverser transcription PCR (RT-PCR) detected CgPGRP-L mRNA expression in circulatory hemocytes, and quantitative real-time RT-PCR revealed that its expression increased after Marinococcus halophilus and Vibrio tubiashii exposure. These results indicate that CgPGRP-L is expressed in hemocytes by bacterial invasion, and then may play roles of a short PGRP and bacterio-lytic lysozyme.