To clarify the effect of 1,3-β-glucan (known as chrysolaminarin) synthase ( Pt BGS) on carbon flow distribution, expression of 1,3-β-glucan synthase gene ( Ptbgs ) was silenced by RNA interference in Phaeodactylum tricornutum . The results showed that the chrysolaminarin content in all transgenic strains was significantly lower than that in the wild-type (WT), while the total lipid content increased to varying degrees. Importantly, the decrease in chrysolaminarin content was significantly correlated with the increase in total lipid content. There was no significant difference in the protein content between all the transgenic strains and WT. Thus, Pt BGS mainly affected the distribution of carbon flow in total lipids and polysaccharides , mainly chrysolaminarin. Silencing Ptbgs changed the fatty acids composition , and specifically promoted polyunsaturated fatty acids production and reduced monounsaturated fatty acids content, but had only a little effect on saturated fatty acids content. Interestingly, the growth of transgenic strains was not influenced while the lipid content increased, indicating that Ptbgs silencing may be an effective strategy to improve lipid production in diatoms. • Distribution of carbon flow can be affected by 1,3-β-glucan synthase ( Pt BGS). • Inhibiting the expression of Ptbgs promoted lipid accumulation. • Silencing Ptbgs changed the fatty acids composition. • Interfering with Ptbgs exerted little effect on growth in Phaeodactylum tricornutum . • Ptbgs silencing may be an effective strategy to improve lipid production in diatoms.