In our study, we have isolated a relatively newly identified bacteria species, Pandoraea pulmonicola YC32, and first assessed its capability to treat malachite green (MG). The effects of various factors on decolorization efficiency were investigated in a batch system. The decolorization efficiency was found to be optimal within a pH of 7-10 and it increased, with increasing initial MG concentration up to 100 mg/l. The relationship between the decolorization rate and MG concentration agreed with Lineweaver-Burk equation. The apparent kinetic parameters, R(MG,max) and K(m), were 6.23 mg-MG/g-cell/h and 153.4 mg/l, respectively. The initial step in the biodegradation pathway of MG by P. pulmonicola YC32 was a reduction or N-demethylation reaction. We achieved a decolorization efficiency of 85.2% with 50mg/l MG in the immobilized P. pulmonicola YC32 continuous column system. This is the first report on the application of a continuous column system to decolorize MG using a microorganism.