The suppression of alternative tissue fates is important for the normal development of an organ. It has been shown that the Polycomb group (PcG) proteins, which are epigenetic regulators, are necessary for transcriptional repression of developmental regulated genes, such as Hox genes. Reductions in PcG protein levels can result in homeotic transformations of the wing, leg and antenna. Despite the importance of the PcG complex in regulating Hox gene expression, its relationship to endogenous gene regulatory networks and its function in tissue/organ fate specification are not well understood. To address this question, we removed Polycomb (Pc) from the developing eye-antennal imaginal disc and observed ectopic expression of the Hox gene Antennapedia (Antp) and the wing selector gene vestigial (vg). These dramatic changes in gene expression accompanied a homeotic transformation of the eye into a wing. The mutant tissue also underwent hyperplastic growth and increased in size by several orders. However, knocking down other PcG proteins was insufficient to induce this phenotype. The Pax6 gene is required for eye formation in all seeing animals from Drosophila to humans. Although previous studies have revealed that Drosophila Pax6 homologs, eyeless (ey) and twin of eyeless (toy) are required for eye specification and head capsule development, the potential roles of Pax6 in the suppression of non-ocular tissue fates remain elusive. We discovered that simultaneous removal of PcG proteins and Pax6 could also induce the eye to wing transformation, indicating Pax6 and PcG proteins cooperate to control growth of the eye and to prevent the establishment of alternative tissue fates. Using different Gal4 drivers, we found that the tissue transformation only happened in the eye progenitor cells ahead of furrow where ey and toy are normally expressed. Removal of Pax6 and PcG proteins in the differentiated photoreceptor cells did not cause the tissue transformation. Moreover, vg was activated mainly in the dorsal part of the eye tissue, when Pax6 and PcG proteins were knocked down using ey-Gal4. This suggests that dorsal section of the eye disc is more capable to transform compared to the ventral domain. We found that the physical transformation of the eye to wing takes place in the third larval instar, when vg was activated ectopically in the eye imaginal disc. However, this transformation requires that PcG proteins and Pax6 are removed from the eye disc starting from the first larval instar stage.