Peptidoglycan recognition proteins (PGRPs) are a family of pattern recognition receptors (PRRs) of the immune system, which bind and hydrolyze bacterial peptidoglycan. Here, a long type PGRP (PGRP-L) was first cloned in the lower vertebrate species Xenopus tropicalis (Xt). The XtPGRP-L possessed a conserved genomic structure with five exons and four introns. The alignment and phylogenetic analysis indicated that XtPGRP-L might be a type of amidase-like PGRP. The 3-D model showed that XtPGRP-L possessed a conserved structure compared with the Drosophila PGRP-Lb. During embryonic development, XtPGRP-L was not expressed until the 72 h tadpole stage. In adult tissues, it was strongly expressed in the liver, lung, intestine, and stomach. Furthermore, after LPS stimulation, the expression of XtPGRP-L was up-regulated significantly in the liver, intestine and spleen, indicating that XtPGRP-L may play an important role in the innate immunity of Xenopus tropicalis.