In Xenopus, six nodal-related genes (Xnrs) have been identified to date. We found numerous tandem duplications of Xnr5 in the Xenopus laevis and Xenopus tropicalis genomes that involve highly conserved copies of coding and regulatory regions. The duplicated versions of Xnr5 were expressed in both the superficial and deep layer of dorsal endoderm and in the deep layer of ventral endoderm, where the initial inducers of mesendoderm formation would be expected to be localized. Overexpression of secreted inhibitors of Xnrs led to a substantially enhanced transcription of the duplicated Xnr5 genes and Xnr6 in embryos. Therefore, Xnr5 and Xnr6 have a novel feedback loop to inhibit transcription of Xnr5 and Xnr6. These results suggest that the initialization of a strong Xnr5 and Xnr6 signal is enabled by the rapid transcription from multiple genes. The novel feedback loop may negatively regulate transcription of Xnr5s and Xnr6 to limit overproduction of these potent inducers, with the Xnr5/Xnr6 signal then activating positive (Xnrs) and negative (Xlefty) loops, which regulate the range of mesodermal tissues produced.