There has been much recent interest in using ionic liquids for processing lignocellulosic biomass. While cellulose has an acknowledged application in generating biofuels, it would be valuable to use the abundant lignin present as well. Rhodococcus has been reported previously to degrade lignin. Therefore, it is attractive to consider a scheme in which an ionic liquid is also used to enhance the microbial breakdown of lignin (bioligninolysis). By using vanillic acid as model compound (Chapter 3), results showed that Rhodococcus UKMP-5M is able to degrade vanillic acid as a sole carbon source at 10mM concentration to give the highest growth rate. An oxygen-dependent reaction degrades vanillic acid into protocatechuic acid and formate in a previously undescribed metabolic pathway. In Chapter 4, GC-MS demonstrated guaiacol as the major product of lignin degradation and the lignin degradation assay indicates that the treatment of lignin with ionic liquids assist the lignin degradation despite some ionic liquids showing a toxicity effect on the cells. Toxicological studies (Chapter 5) demonstrated different ionic liquids show varying toxicity to the bacteria. By using classical disk diffusion test in screening 16 different ionic liquids, it was revealed that the toxicity is correlated with the size of the ionic alkyl chain; however, the carbon atom count, not the structure or the distribution of those atoms in the cation, correlates directly with the toxicity. The strongest link was discovered with pH effects rather than with structure in the toxicity of acidic ionic liquids. We also propose that the octanol-water partition coefficient (Kow) has the controlling impact on the toxicity of ionic liquids. Bacterial growth curves exhibited three different trends: a complete inhibition, an increase in toxicity with an increase of ionic liquid concentration and the extension of the lag phase due to bacterial adaptation. This study established that Rhodococcus UKMP-5M could adapt and grow in the presence of ionic liquids with 1-ethyl-3-methylimidazolium acetate, [Emim][OAc] as the most promising candidate in designing an ionic liquid-facilitated system of bioligninolysis.