Autochthonous bacteria associated with browning in moromi fermentation were investigated, isolated and characterised. By cultured plating, only Bacillus spp. and Staphylococcus spp. were mainly observed. By reverse transcriptase-nested PCR-DGGE (RevT-nested PCR-DGGE), lactic acid bacteria (LAB) were primarily observed while Bacillus spp. and Staphylococcus spp. were only observed in particular stages of fermentation. The change of Maillard's reactants, particularly xylose and amino acids, as well as browning indicator were significant, when Bacillus and Staphylococcus were the main bacteria as mapping by RevT-nested PCR-DGGE. Extremely low browning indicator was found in moromi with more diverse autochthonous strains including Bacillus amyloliquefaciens, B. zhangzhouensis, B. pumilus, B. infantis S. condiment, Staphylococcus sp., S. carnosus, S. epidermidis and S. xylosus. Staphylococcus sp. SSB48, and B. amyloliquefaciens SSB6, with ability to ferment xylose and degrade melanoidin, were selected to test in moromi. These two isolates significantly reduced browning in moromi through melanoidin degradation without interfering with aromatic complexity and showed the best result in mature moromi fermented for one month. This study demonstrated the efficient method and potential source of target strains with novel properties. Additionally, the application of these autochthonous isolates was one of the potentially new biological means for browning reduction in soy sauce.