Identifying microalgae biodiversity is essential to unleashing the diverse potential applications for microalgae. The aim of the chapter is to define the various tools and methodologies possible for revealing microalgae diversity. Identifying microalgae from natural environments, hotspots, and extreme environments enables us to isolate naturally tolerant species that may thrive and exhibit unique characteristics. Identifying microalgae will enable researchers to uncover new applications for these versatile organisms, including biofuel production, wastewater treatment, and pharmaceutical development. Hence, it is crucial to define the different possible identification approaches, beginning with the sample collection protocols and extending to the identification methods employed to determine the diversity of microalgae in an ecosystem.