The integration of computational and molecular modeling techniques in algae research has significantly advanced the global understanding of the therapeutic potential of algae-derived compounds. Molecular docking and molecular dynamics simulations have emerged as essential tools in drug discovery, enabling researchers to predict binding affinities, elucidate mechanisms of action, and identify promising drug candidates from the vast array of bioactive compounds found in algae. Identification and characterization of several algae-derived therapeutic agents have been reported as potent management agents for a vast number of human diseases, including genetic, neurodegenerative, metabolic, cancer, infectious, viral diseases, and so on, using molecular dynamics and docking approaches. Despite the challenges in optimizing cultivation, extraction processes, and ensuring safety and efficacy, the prospective of algae in discovering novel therapeutic agents remains immense. Future research focuses on high-throughput screening, metabolic engineering, and the introduction of artificial intelligence to enhance the discovery of algae-based drugs. With continued advancements in computational methodologies and experimental validation, algae are poised to be very important in addressing various human health challenges, paving the way for innovative therapeutic solutions. This chapter enumerates the evidential importance of integrating ligand-centric docking and atomistic simulations approaches in algae research. The chapter concludes with suggested future directions of computational molecular modeling in algae research.