Galactomyces geotrichum MTCC 1360 showed 87 % decolorization of the azo dye Rubine GFL (50 mg l(-1)) within 96 h at 30 °C and pH 7.0 under static conditions, with significant reduction of chemical oxygen demand (67 %) and total organic carbon (59 %). Examination of oxidoreductive enzymes, namely laccase, tyrosinase and azo reductase, confirmed their role in decolorization and degradation of Rubine GFL. Biodegradation of Rubine GFL into different metabolites was confirmed using high-performance TLC, HPLC, Fourier transform IR spectroscopy and GC-MS analysis. During toxicological studies, cell death was observed in Rubine GFL-treated Allium cepa root cells. Toxicological studies before and after microbial treatment were done with respect to cytotoxicity, genotoxicity, oxidative stress, antioxidant enzyme status, protein oxidation and lipid peroxidation using root cells of A. cepa. The analysis with A. cepa showed that the dye exerts oxidative stress and subsequently has a toxic effect on the root cells, whereas its metabolites are less toxic. Phytotoxicity studies revealed the less toxic nature of the metabolites as compared with Rubine GFL.