Owing to their remarkable physical-chemical properties, Ionic Liquids are considered as very promising capturing/transportation fluids in biotechnological applications for gaseous pollutants such as Carbon dioxide (CO2) which can be then remediated by living microorganisms. However, Ionic Liquids are also toxic towards the majority of living species used for remediation purposes among green microalgae. In this study different ionic liquids were tested for their toxicity for different concentrations on one type of commonly used green microalgae, Botryococcus braunii. Ionic liquids bearing long alkyl chain do display higher CO2 uptake than ioni liquids analogue bearing shorter alkyl chain. This might explain why the production of biomass is dramatically enhanced with 1-octyl-1-Methyl Piperidinium bis (trifluoromethylsulfonyl) imide OMPipNTf2 compared to 1-Butyl-1-Methyl Piperidinium bis(trifluoromethylsulfonyl) imide BMPipNTf2 as the latter can supply more CO2 to the microalgae than the former leading to enhanced organism growth. © 2016 The Authors.