E. coli fumarate nitrate reductase (FNR) binds to conserved FNR sites to regulate transcription under anaerobic condition. L. lactis subsp. cremoris MG1363 strain contains two FNR-like proteins (FlpA and B) encoded by flpA and flpB genes and the rcfA gene-encoded RcfA in L. lactis subsp. lactis IL1403 strain. Potential FNR-binding sites were located upstream of these genes. The flpA promoter is expressed in MG1363 anaerobically and aerobically. The flpB and rcfA promoters have typical class II FNR-dependent promoters and are activated anaerobically in MG1363 and IL1403, respectively. Despite their strong homology, the Flp and RcfA proteins cannot substitute for each other and control these promoters in the heterologous strains. The flpA and flpB promoters require FlpA and FlpB for activation in the MG1363 background. This was confirmed by expressing FlpB under nisin control in flp mutants and monitoring flpA promoter expression. In flpB(-) backgrounds, both FlpA and FlpB were required for flpA promoter expression. FlpB could not complement for the lack of FlpA protein in flpA(-) backgrounds.