This study focuses on the nucleic acid-based detection of microalgae associated with plants, employing a comprehensive methodology for accurate identification and quantification. Samples are collected from various plant-associated environments, and nucleic acids are extracted using a protocol. Polymerase chain reaction (PCR) with specifically designed primers targeted unique genetic sequences of the microalgae of interest. DNA abundance is quantitatively assessed using real-time PCR (qPCR). Additionally, probe-based assays, including fluorescence in situ hybridization (FISH) are explored for direct visualization and quantification. DNA sequencing provided in-depth genetic information, confirming microalgal species identity. Bioinformatics analysis further elucidated the genetic characteristics of the identified microalgae. Rigorous validation, including positive and negative controls, ensured assay specificity and sensitivity. The study offers a strong framework for nucleic acid-based detection of plant-associated microalgae, contributing to a better understanding of their ecology and potential implications for plant health.