SET and RING-finger-associated (SRA) protein is involved in establishment and/or maintenance of DNA methylation in eukaryotes.It recognizes and flips out 5-methylcytosine from DNA backbone via its SRA domain.Here we identified two SRA domain-containing proteins Sco5333 and Tbis1 in bacteria which are both associated with a distinct HNH motif.Either Sco5333 in dimer or Tbis1 in monomer specifically binds to 5mC in all DNA sequence contexts.Tbis1 has a bias of～1000folds in binding affinity for fully-methylated DNA over non-methylated one.Calorimetric measurement revealed that one molecule of DNA,either fully-or hemimethylated,was bound by two SRA domains (or one dimeric Sco5333) with a dissociation contant (KD) of 1.47～4.13μM,very close to that of SUVH5.Structural modelling and superposition suggested that both proteins employ dual flip-out mechanism as eukaryotic SRASUVH5.