Species domestication and improvement were decisive in increasing agricultural production yields. The microalgae industry must now realize the same accomplishment to boost its development instead of only using wild strains. Although genetically engineering microalgae is a promising path to explore, the artificial modification of the microalgae genome can have adverse side-effects on biomass productivity. Here, we propose a Darwinian method to select and improve microalgal strains, exploiting the competitive exclusion principle in a dynamical environment to drive evolution. Choosing an appropriate selection pressure allows a new adapted population having enhanced properties to emerge. In a natural growing environment, light intensity is consistently changing due to meteorological events, differing microalgae concentration and other exogenous factors. Consequently, the pigmentary profile regulation and the associated genetic mechanism is highly modulable in most microalgae. On top of this, high light intensities are known to elicit strong cellular stresses. For these reasons, a dynamical light regime with high light intensities was deemed a potentially efficient selection factor for the emergence of a new strain adapted to higher irradiance levels. Following 160 days of selection under variable light intensity the biomass productivity of Tisochrysis lutea increased by 77%. Genetic analyses further confirmed the selection protocol's success, with the apparition of 2716 new alleles. To our knowledge, this is the first selection approach allowing a significant biomass productivity increase resulting from an enhanced capacity of microalgae pigment photoadaptation.