Microalgae are a common species found in freshwater areas as well as seashores. Microalgae are different from the nature of the microorganisms, differences such as morphology, physiology and the genetics of them. Microalgal samples were collected from Thirumoorthymalai Hills freshwater and are characterized by morphological and sequencing of 16s ribosomal DNA. The sequence revealed that four samples were Leptolyngbya subtilis, Leptolyngbya sp, Oscillatoria tenuis, and Phormidium sp. based on genetic similarity. These microalgae were cultivated and their bioactive compounds were analyzed by using GC-MS and FTIR, which shows that these Microalgae have vital bioactive metabolites which may have antimicrobial activity, anti-inflammatory activity, and anti-cancer activity.