Three halotolerant bacteria were isolated from seawater collected along the Red sea coast, Jeddah, KSA and evaluated for their capacity to remove congo red (CR) and malachite green (MG), commonly used in paper printing and textile factories. Mixture design and response surface methodology (RSM) based on statistical design of experiments were applied to explore the region of interest and interaction between the three selected strains. Color removal were confirmed by UV–visible and Fourier transform infrared spectroscopy analysis (FTIR). Microbial enzymes related to dyes degradation were also investigated after analysis of the whole bacterial genome. Results, showed that the dye degrading strains were identified as Klebsiella pneumoniae K2, Enterobacter sp. K16b and Vibrio tritonius K20. The effect of K. pneumoniae K2, Enterobacter sp. K16b and V. tritonius K20, tested separately, induced a maximum of decolorization of 74.54%, 85.71% and 82.73% for CR and 72.67%, 74.26% and 72.73% for MG, respectively. Process optimization, showed that the higher decolorization (%) of CR and MG yields were obtained when the proportions of K. pneumoniae K2, Enterobacter sp. K16b and V. tritonius K20 were 21.34%, 56.35% and 22.30% for CR and 42.38%, 56.56% and 0.10%, for MG. Biodegradation of dyes was confirmed by UV–Vis spectrum and FTIR analysis. The phytotoxicity assay revealed that when the irrigation medium was supplemented with extract obtained from the respective microbial treated dyes solutions, seed germination, shoot and root lengths were not affected, indicating that selected strains have the ability not only to remove color but also to detoxify dyes solutions. Whole genome analysis confirms the presence of a valuable enzymes (reductase, dehydrogenase, kinase, hydrolase, transferase, catalase and, dioxygenase enzymes) involved in chemicals degradation, suggesting that they might be useful in biological treatment of various coloured industrial effluents.