Among the members of the Drosophila melanogaster vitelline membrane protein gene family, VM32E has the unique feature of being a component of both the vitelline and the endochorion layers. The VM32E gene is expressed at stage 10 of egg chamber development in the main body follicle cells, and it is repressed in the anterior and posterior follicle cells. Here, we show that this spatial restriction of VM32E gene expression is conserved in the D. pseudoobscura orthologous gene, suggestive of a conserved function of VM32E protein. The VM32E gene is not expressed in the centripetal migrating follicle cells, where the Decapentaplegic (Dpp) pathway is active in patterning the anterior eggshell structures. By analyzing the native VM32E gene and the activity of specific VM32E regulatory regions, in genetic backgrounds altering the Dpp pathway, we show that VM32E gene is negatively regulated by the Dpp signaling. Therefore, it appears that the Dpp signaling pathway executes its control on eggshell morphogenesis also by controlling the expression of eggshell structural genes.