How organ identity is determined is a fundamental question in developmental biology. In Drosophila, field-specific selector genes, such as eyeless (ey) for eyes and vestigial (vg) for wings, participate in the determination of imaginal disc-specific identity. We performed gain-of-function screening and identified a gene named winged eye (wge), which encodes a bromo-adjacent homology domain protein that localizes at specific sites on chromosomes in a bromo-adjacent homology domain-dependent manner. Overexpression of wge-induced ectopic wings with antero-posterior and dorso-ventral axes in the eye field in a region-specific Hox gene-(Antennapedia) independent manner. Overexpression of wge was sufficient for ectopic expression of vg in eye discs. A context-dependent requirement of wge was demonstrated for vg expression in wing discs and for expression of eyes absent (eya), a control gene for eye development downstream of ey, in eye discs. In contrast to vg, however, overexpression of wge inhibited EY-mediated expression of eya. Consistent with colocalization on polytene chromosomes of WGE and Posterior sex combs (PSC), a Polycomb group gene product, we demonstrated an antagonistic genetic interaction between wge and Psc. These findings suggest that wge functions in the determination of disc-specific identity, downstream of Hox genes.