Two genes that are highly expressed in the tomato shoot apex have been cloned by differential hybridization. One of the deduced polypeptides (AT1) shows significant similarities to class II proteinase inhibitors, while the other (AT2) displays similarities to defensins. Transcripts of both genes are also detectable in the developing flower and are present only in minor amounts in other tissues tested. In situ hybridization analysis revealed that both genes are expressed in non-overlapping subsets of cells in the shoot apex, as well as in the developing flower. The potential use of these genes as markers for certain cell types and the possible biological function of the encoded proteins are discussed.