The structure and function of the amelogenin gene on a tooth germs in the frog Xenopus tropicalis, were examined. Using PCR, we observed an intensive band of amelogenin in maxillas with teeth but not in the toothless mandibles, and in situ hybridization revealed the restricted expression of amelogenin only in secreting ameloblasts in a tooth germs. Sequence analyses indicated that two types of amelogenin mRNA were alternatively spliced and derived from a single gene. They are referred to here as amelogenin mRNA-A and -B. In unique 5'-UTR, mRNA-A has a long exon 1, which is much longer than the same exon in other animals' amelogenin, and both mRNA-A and -B possesses new exons, referred to here as exon 2a and 2b. The following protein coding region was divided into five exons, as in the case of another frog, Xenopus laevis, whose amelogenin sequence was closest to X. tropicalis, and the amelogenin of X. tropicalis may play a role in enamel formation, as in other animals. A pair of amelogenin mRNAs of X. tropicalis have the most primitive sequence among known mRNAs and, in particular, the extremely long exon 1, and the newly found exons 2a and 2b , may be key in exploring the archetype of amelogenin mRNA.