The current chapter discusses the rapid detection and identification of microalgae using colony PCR. Microalgae are photosynthetic organisms capable of nitrogen fixation, photosynthesis, and adaptation to varying environmental conditions, making them highly valuable. Colony PCR is a valuable molecular biology technique used for the rapid identification of microalgal species. Colony PCR replaces conventional DNA isolation procedures with a technique where a single colony is used as a template for amplification using PCR. In the present study, a novel approach using a simple glass grinding method for single colony PCR was employed, providing a dependable and rapid protocol for microalgal genomics applications. This method will help in the identification of microalgal species more effectively and moreover an efficient alternative for conventional DNA isolation techniques.