Expression of the Bacillus subtilis gluconate (gnt) operon is negatively regulated by the gnt repressor which is antagonized by D-gluconate or D-glucono-delta-lactone. The repressor specifically binds to a gnt operator near the gnt promoter. From the results of gel retardation assaying of the gnt repressor and various restriction enzyme digests of a fragment carrying the gnt promoter and the gntR gene, the gnt operator was found to be located within a 141-base pair region containing the gnt promoter. Deoxyribonuclease I protection experiments revealed that the gnt repressor protected a gnt promoter region, between -10 and +15, which contains a region showing dyad symmetry with a sequence showing half-symmetry, ATACTTGTA. A 35-base pair synthetic duplex DNA containing this region showing dyad symmetry specifically bound to the gnt repressor. Through cleavage at two AccI sites in the protected region an 8-base pair deletion was introduced into the region showing dyad symmetry, which made expression of the gnt promoter constitutive. A DNA fragment carrying this deletion did not bind to the repressor. These results clearly indicated that the gnt operator sequence is a sequence containing the region showing dyad symmetry located at the transcription initiation site of the gnt operon. It was also suggested that the gnt operon contains only one operator. The similarity in the recognition between the repressor-operator interaction of the gnt operon and those of Escherichia coli TrpR and its operators was discussed.