Objective To investigate the changes in the surface-associated protein expression of streptococcus rnutans (Sm) isolated from clinical samples at pH7.0 and pH5.0. Methods The proteins were extracted from cells at pH7.0 and pH5.0 by Homer method. The proteins were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis followed by image analysis. Proteins were identified by matrix-assisted la?ser desorption ionization time of flight mass spectrometry and computer-assisted protein sequence analysis. Results Image analysis revealed that four high expression levels of protein loci and two specific protein loci were existed in two strains at pH7.0. Two high expression levels of protein loci and two specific protein loci were existed in two strains at pH 5.0. Three high expression levels of protein loci and six specific protein loci were existed in Sm593 at pH5.0. Two-component system histidine kinases Lyts and glyceraldehyde-3-phosphate dehydrogenase were highly modulated, and NADH oxidase were modulated specifically. Conclusion The two clinical isolations in acid have high expression of some special proteins, which are presumed to be the resemblance of acid reaction.The difference of protein expression of two clinical isolations in acid may represent their distinct acid resistance.