Many of the bioactive substances used in pharmaceutical industry are easily affected by temperature, light and oxygen, and are easily degraded during storage and processing, and exhibit poor adsorption properties during digestion, which limits their direct use. Microalgae are rich in oils which have antimicrobial properties and antioxidants that attract attention in both food and pharmaceutical sectors in recent years. Studies to encapsulate bioactive compound-rich microalgae oils with nanotechnological approaches to improve the physical and chemical stability are relatively new, and it is promising to apply these approaches for pharmaceutical purposes. In this study, cytotoxic effects of oil extracts of Botryococcus braunii and Microcystis aeruginosa and their oil-loaded nanoparticles on L929 cell line, PC-3 prostate cell line, SHSY-5Y neuroblastoma cell line and AGS gastric adenocarcinoma cell line were investigated. The obtained extracts were found to have no cytotoxic effect on L929 cells. However, they showed cytotoxic effect on cancer cells. As for the nanoparticles; a gradual release was determined and the stability of the nanoparticle structure was shown. In the light of obtained findings, it was considered that nanoparticles produced with oil extracts of microalgae which have bioactive substances, have potential to be evaluated especially in pharmaceutical and cosmetic fields.