Background The release of triphenylmethane dyes, like malachite green (MG) and crystal violet (CV), into the environment is a cause of concern due to its toxicity, mutagenicity and carcinogenicity. Result A bacterial strain that is capable of decolorizing both dyes was isolated from the composted neem oil-seed cake. The strain was characterized as Stenotrophomonas maltophilia based on the 16S rRNA gene sequence and designated as isolate TPMD-1. The kinetic study of the dye degradation revealed the efficiency of the above isolate to degrade MG. The effect of substrate concentration, pH, temperature, and agitation on the decolorization of MG by the isolate was also studied. The MG degradation rate was slightly more in neutral pH at 28–30 °C and 150 rpm. The UV-spectroscopy, HPLC, and FTIR analyses of the dye sample before and after bacterial treatment revealed the high ability of S. maltophilia TPDM-1 in the removal of MG from the media. The genetic snapshot of the isolate by PCR amplification and sequencing showed the presence of genes 'lac’ and ‘tmr’ that codes for laccase and triphenylmethane reductase. Conclusion This study presented the first report of Stenotrophomonas maltophilia in the degradation and detoxification of MG dye by oxidoreduction, which could be used for the bioremediation of aquatic environments contaminated by MG.