Background While many developmentally relevant enhancers act in a modular fashion, there is growing evidence for nonadditive interactions between distinct cis‐regulatory enhancers. We investigated if nonautonomous enhancer interactions underlie transcription regulation of the Drosophila segment polarity gene, wingless. Results We identified two wg enhancers active at the blastoderm stage: wg 3613u, located from −3.6 to −1.3 kb upstream of the wg transcription start site (TSS) and 3046d, located in intron two of the wg gene, from 3.0 to 4.6 kb downstream of the TSS. Genetic experiments confirm that Even Skipped (Eve), Fushi‐tarazu (Ftz), Runt, Odd‐paired (Opa), Odd‐skipped (Odd), and Paired (Prd) contribute to spatially regulated wg expression. Interestingly, there are enhancer specific differences in response to the gain or loss of function of pair‐rule gene activity. Although each element recapitulates aspects of wg expression, a composite reporter containing both enhancers more faithfully recapitulates wg regulation than would be predicted from the sum of their individual responses. Conclusion These results suggest that the regulation of wg by pair‐rule genes involves nonadditive interactions between distinct cis‐regulatory enhancers.