In a context of human population increase and depletion of terrestrial resources, exploitation of microalgae is an ecofriendly alternative path for the future. Currently, microalgae are used in many areas domain like food, feed, bio-remediation, health industry and third generation biofuels. Yet, until now, all cultivated microalgae strains are derived directly from their natural environment. One way of improving productivity is the acquisition of selected algae strains with improved capabilities. In this study, we show that the intra-strain diversity in microalgae can be exploited to produce improved strains. An improved strain with high neutral lipid productivity was obtained, which could be used, for example, for feed or bio-fuels applications. This study also shows the necessity to study and exploit biodiversity within microalgae specie. In addition, we obtained drafts genomes and phenotypic comparisons between the wild-type and the improved clonal strains. These results reflect the origin of intra-strain diversity and microalgae adaptive capacity. The clonal strain selected accumulates more lipids, at the expense of carbohydrates. The numerous patterns of transposable element activity suggest that it is the main driver of this adaptation.