The aim of this study was to investigate the possible interference of anionic and cationic flocculants in the lipid extraction and fatty acid profiles of two species of marine microalgae: Nannochloropsis oculata and Thalassiosira weissflogii. Cells were grown in batch cultures (f/2 medium, salinity of 28, temperature of 20 °C, light intensity of 40 μmol photons m-2 s-1 and 12/12 h L/D photoperiod) and concentrated using sodium hydroxide (control), sodium hydroxide and the anionic polyacrylamide flocculant Magnafloc® LT-25 (APF treatment) and sodium hydroxide plus the cationic polyacrylamide flocculant Flopam® (CPF treatment). There were no statistically significant differences among treatments with respect to lipid extraction for both species. However, N. oculata which presented higher percentages of C16:0, C16:1 and C20:5 fatty acids showed an increase of C14:0 and a decrease of C20:5 with the use of anionic flocculant. Additionally, T. weissflogii which had high percentages of C16:0, C16:1, C16:3 and C20:5, showed a decrease of C18:0 and C18:1n9c when both flocculants were used and a small decrease of C16:0 in the APF treatment. The results indicate that the choice of flocculant should be based on the level of saturation desirable, i.e., if the goal is to produce more stable biodiesel, with low percentage unsaturated fatty acids, then anionic flocculants should be used. On the other hand, if the aim is to produce unsaturated fatty acids for commercial uses in the pharmacy or food industries, then anionic polymers should be avoided.