The concept of producing renewable microalgae biomass using as a main nutrient source a secondary wastewater stream is presently under investigation. It is planned to purify the wastewater by the growth of algal biomass while producing a feedstock that can be used for the bioenergy sector. If important biomass density is achieved, this strategy will be adopted in a novel process named SunCHem (proposed at the EPFL-PSI SWT group) using hydrothermal treatment of microalgae to produce methane. By coupling the wastewater treatment, the capture of CO2 emissions and the production of methane through microalgae, we directly impact the sustainable use of carbon resources. In this work, we aim to develop a strategy for the genetic improvement of microalgae in order to enhance the accumulation of carbon inside the cells. The strategy contributes to efficiently obtain a significant change in the production of algal biomass and thus potentially, to increase the methane production yields. The strains Chlorella sp. andScenedesmus sp. have been used to apply the modification of genes involved in these metabolic pathways; in particular, the genes codifying for the glutamine synthetase (glnA). Chlorella sp. was isolated from the wastewater treatment plant and adapted for axenic culturing. These microalgae were also selected due to an appropriate carbon balance for their future hydrothermal conversion into methane.