In this study we used a newly isolated Yarrowia lipolytica ISF7 strain with a unique capacity to remove malachite green from culture. The effects of operating parameters such as initial pH, dye concentration, temperature and time added on the MG biosorption were studied using response surface methodology, a total of 32 experimental runs were set and the experimental data fitted to the empirical second-order polynomial model of a suitable degree. The optimum biosorption conditions were determined as initial pH7.0, temperature 25°C, 24h and 35mgL−1 of MG concentration. The maximum adsorption capacity for biosorption was found around the pH range 6.5–7.5. Hence from the obtained results it is clear that the noxious dye removal percentage is very low in acidic pH below 5 and alkaline pH above 7.5. The adequate precision (AP) ratio of the models varies between 34.22 for %R MG, which is an adequate signal for the model. AP values higher than 4 are desirable, and confirm that the predicted models can be used to navigate the space defined by the CCD. The nature of biomass dye interactions was evaluated by FT-IR analysis and maximum MG removal (99.889%) was obtained under optimum conditions.