In this study we have investigated the molecular background of the previously reported dye decolourization potential of Bacillus sp. LD003. Strain LD003 was previously isolated on Kraft lignin and was able to decolourize various lignin model dyes. Specifically Azure B (AB) was decolourized efficiently. Proteins possibly involved in AB decolourization were partially purified, fractionated by gel electrophoresis and identified via mass spectrometry. Five candidate enzymes were selected and expressed in Escherichia coli. Of these, only a quinone dehydrogenase was shown to decolourize AB. Thus, this quinone dehydrogenase was identified as an AB decolourizing enzyme of Bacillus sp. LD003.