Microalgae technology is a promising alternative feedstock for biodiesel production. Chlamydomonas reinhardtii is a unicellular green alga, one of the most important model organisms, that can produce increased lipid yields under abiotic conditions. In this study we show that treatment with 0.1 M of NaCl rapidly raises the amount of neutral lipids in C. reinhardtii, without impairing cellular growth rate, being, therefore, a favorable condition for biomass and energy production. A nuclear proteomic analysis was conducted on salt stress to better understand the molecular mechanism and the regulatory proteins involved in the adaptation to salt stress and increased lipid yields.