Herbaspirillum seropedicae is an associative, endophytic non‐nodulating diazotrophic bacterium that colonises several grasses. An ORF encoding a LysR‐type transcriptional regulator, very similar to NodD proteins of rhizobia, was identified in its genome. This nodD ‐like gene, named fdeR , is divergently transcribed from an operon encoding enzymes involved in flavonoid degradation ( fde operon). Apigenin, chrysin, luteolin and naringenin strongly induce transcription of the fde operon, but not that of the fdeR , in an FdeR‐dependent manner. The intergenic region between fdeR and fdeA contains several generic LysR consensus sequences (T‐N ₁₁ ‐A) and we propose a binding site for FdeR, which is conserved in other bacteria. DNase I foot‐printing revealed that the interaction with the FdeR binding site is modified by the four flavonoids that stimulate transcription of the fde operon. Moreover, FdeR binds naringenin and chrysin as shown by isothermal titration calorimetry. Interestingly, FdeR also binds in vitro to the nod ‐box from the nodABC operon of Rhizobium sp. NGR234 and is able to activate its transcription in vivo . These results show that FdeR exhibits two features of rhizobial NodD proteins: nod ‐box recognition and flavonoid‐dependent transcription activation, but its role in H. seropedicae and related organisms seems to have evolved to control flavonoid metabolism.