Algae present an attractive source of bioactive chemical substances with the potential to produce various compounds with applications in food, cosmetics, and medicine. The desire for natural bioactive substances is rising due to the adverse side effects of current chemosynthetic medications and the pursuit of wellness. It is widely acknowledged that algae are a rich source of fatty acids, pigments, and other high-value-added compounds. Based on epidemiological investigations, bioactive compounds have been found to reduce the risk of neurodegenerative diseases and chronic illnesses like diabetes, cancer, and hyperlipidemia. The physiological functions of these essential compounds, including anti-cancer, anti-diabetic, immune-modulating, and neuroprotective agents, generate more interest. The abundance of bioactive substances found in algae, which have been thoroughly documented in recent studies, has been obtained by researchers due to advancements in extraction methods and environmentally sustainable methodologies. However, there is still a need for more information in the literature regarding the instruments and analytical techniques that should be used to detect and examine the compounds in the algae-based extracts to ensure their quality. To investigate algae bioactive compounds thoroughly, this chapter explores the latest advances in analytical techniques. It integrates spectrometry with sophisticated molecular techniques, including transcriptomics, proteomics, and metabolomics. The combination of advanced spectrometry, proteomics, and genomics provides a comprehensive strategy for improving our understanding of algal bioactive compounds. It provides a platform for discovering new biomolecules with potential roles in environmental biotechnology, nutraceuticals, and pharmaceuticals. This holistic strategy lays the foundation for innovative and sustainable algal utilization of resources.