Cyanobacteria, commonly known as blue-green algae, have been pivotal components of Earth’s ecosystems for billions of years, demonstrating widespread ecological impacts across various habitats. They play a crucial role in terrestrial ecosystems because of their exceptional capacity to promote stress tolerance, growth factor production, phosphorus enhancement, nitrogen fixation, and plant health and development. The genetics of cyanobacteria that aid in plant growth are examined in this chapter, with a focus on isolating genomic DNA. The long history and notable effects on the environment of cyanobacteria are well known. They are necessary for nutrient cycling, soil fertility, and sustainable agriculture. The protocol outlined combines established methodologies with the latest molecular biology techniques, offering a comprehensive guide for researchers. From cultivation to genomic DNA isolation, the process involves key steps such as cell lysis, phase separation, and precipitation. This work aims to bridge the gap between theoretical understanding and practical application, providing insights into the molecular foundations of cyanobacteria–plant interactions and advancing the exploration of their genomic landscape.