Fibronectin-binding proteins A and B (FnBPA and FnBPB) mediate adhesion ofStaphylococcus aureusto fibrinogen, elastin and fibronectin. FnBPA and FnBPB are encoded by two closely linked genes,fnbAandfnbB, respectively. With the exception of the N-terminal regions, the amino acid sequences of FnBPA and FnBPB are highly conserved. To investigate the genetics and evolution offnbAandfnbB, the most variable regions, which code for the 67th amino acids of the A through B regions (A67–B) offnbAandfnbB, were focused upon. Eighty isolates ofS. aureusin Japan were sequenced and 19 and 18 types infnbAandfnbB, respectively, identified. Although the phylogeny offnbAandfnbBwere found to be quite different, eachfnbAtype connected with a specificfnbBtype, indicating thatfnbAandfnbBmutate independently, whereas the combination of both genes after recombination is stable. Hence thosefnbA–fnbBcombinations were defined as FnBP sequence types (FnSTs). Representative isolates of each FnST were assigned distinct STs by multilocus sequence typing, suggesting correspondence of FnST with genome lineage. Linkage disequilibrium (LD) analysis of the A67–B region revealed that subdomains N2, N3 and FnBR1 form a LD block infnbA, whereas N2 and N3 form two independent LD blocks infnbB. N2–N3 three-dimensional structural models indicated that not only the variable amino acid residues, but also well-conserved amino acid residues between FnBPA and FnBPB, are located on the surface of the protein. These results highlight a molecular process of the FnBP that has evolved by mingled mutation and recombination with retention of functions.