The role and benefits of omega-3 fatty acids in normal development as well as in variety of disease conditions have been well established. Omega-3 fatty acids which include alpha-linolenic acids (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) need to be taken as dietary supplements as the human body is unable to synthesize them. Fish remains the major source and alternatives to fish sources such as algae need to be explored to fulfill the increasing demand for omega-3 fatty acids. Recent advancements in artificial intelligence (AI) have been explored for classifying the oils containing omega-3 fatty acids. However, advances in multiomics (genomics, transcriptomics, proteomics, etc.) can provide vital system-level insights about omega-3 fatty acid-producing algae. Leveraging AI with a systemic biology approach can pave the way to generate key insights on bioprocess development as well as strain development for omega-3 fatty acids. Applications of AI tools need to be explored further for omega-3 fatty acids and can revolutionize the field by helping overcome the bottlenecks.