SAP18, a polypeptide associated with the Sin3–HDAC co‐repressor complex, was identified in a yeast two‐hybrid screen as capable of interacting with the Drosophila GAGA factor. The interaction was confirmed in vitro by glutathione S‐transferase pull‐down assays using recombinant proteins and crude SL2 nuclear extracts. The first 245 residues of GAGA, including the POZ domain, are necessary and sufficient to bind dSAP18. In polytene chromosomes, dSAP18 and GAGA co‐localize at a few discrete sites and, in particular, at the bithorax complex where GAGA binds some silenced polycomb response elements. When the dSAP18 dose is reduced, flies heterozygous for the GAGA mutation Trl67 show the homeotic transformation of segment A6 into A5, indicating that GAGA–dSAP18 interaction contributes to the functional regulation of the iab‐6 element of the bithorax complex. These results suggest that, through recruitment of the Sin3–HDAC complex, GAGA might contribute to the regulation of homeotic gene expression.