Proper tissue patterning is an essential step during organ formation. During this process, genes are expressed in distinct patterns, defining boundaries for future functional domains. The bone morphogenetic protein (BMP) signaling pathway sets the anterior domain during eggshell patterning. Previously, the homolog of BMPR2, Wishful thinking (WIT), was shown to be required for BMP signaling and patterning during eggshell formation. Expressed in a conserved anterior pattern, the width of patterning in the follicular epithelium is evolutionarily divergent between species. We used genome editing to demonstrate how the gene pattern divergence is controlled in within the locus of Furthermore, unlike direct targets of BMP signaling, we demonstrate how one transcription factor binding site shapes the pattern of WIT in by negative regulation. However, changes in this site are not sufficient to explain the evolution of patterning, suggesting that a positive regulatory element that controls pattern divergence remains to be discovered.