<p>This review explores the biological rhythms of eukaryotic microalgae, focusing on chlorophytes, diatoms, and dinoflagellates and their applications in biotechnology and ecology. Eukaryotic microalgae, which are crucial primary producers in aquatic ecosystems, exhibit complex biological rhythms that synchronize physiological processes such as photosynthesis, cell division, and nutrient metabolism with environmental cycles. These rhythms have been shown to enhance microalgal adaptability and productivity, making them valuable for industrial applications, including biofuel production and synthesis of high-value compounds. However, due to the diversity of microalgal species and the limited number of species with fully sequenced genomes, the precise identification of circadian components remains a challenge. Despite these challenges, advances in molecular tools and biotechnological applications continue to improve our understanding of microalgal rhythms and their potential for enhancing biomass productivity. This review highlights the importance of further research on the genetic and molecular mechanisms underlying these rhythms to fully exploit their biotechnological and ecological potential.</p>