Abstract: Strain Chlorella hirataii was used as the starting strains for genome shuffling. They were mutated by UV-light and ethylmesylate separately, and four mutant strains with increased lipids yield were selected.Two rounds of genome shuffling were carried out with the four mutant strains using PEG to mediate protoplasts fusion. Finally, the Chlorella hirataii F2 C2 was selected which produced lipids ( 59.01%) higher than the original strain by 101.4%. Compare with the original strain in the same batch, the total lipid composition of the Chlorella hirataii F2 C2 didn't change a lot, but there was a big gap between the content of each component.