Microalgae are microscopic organisms that are unicellular, occurring singly or in connected communities at aquatic habitats. Morphological features and pigment profiles have served as the primary tools for classifying microalgal species throughout history. In cases where morphological features are insufficient for definitive identification of microalgae, molecular determination techniques demonstrate exceptional effectiveness, particularly for pico-sized algae. So, optimized technique in extracting DNA from microalgae plays a crucial role in analyzing the taxonomic significance of microalgae. The present protocol demonstrates a modified technique for effective isolation of genomic DNA from microalgae and cyanobacteria.