The vast, untapped potential of the world’s oceans is revealing groundbreaking advancements in human health and vaccination. Microalgae such as Nannochloropsis spp. and Dunaliella salina are emerging as resources for recombinant vaccine development with specific and heterologous genetic tools used to boost production of functional recombinant antigens in Dunaliella salina and Nannochloropsis spp. to induce immunoprotection. In humans, several antigens produced in microalgae have shown potential in combating diseases caused by the human papillomavirus, human immunodeficiency virus, hepatitis B virus, influenza virus, Zika virus, Zaire Ebola virus, Plasmodium falciparum, and Staphylococcus aureus. For animals, microalgae-derived vaccine prototypes have been developed to fight against the foot-and-mouth disease virus, classical swine fever virus, vibriosis, white spot syndrome virus, and Histophilus somni. Marine organisms offer unique advantages, including the ability to express complex antigens and sustainable production. Additionally, the oceans provide an array of bioactive compounds that serve as therapeutics, potent adjuvants, delivery systems, and immunomodulatory agents. These innovations from the sea not only enhance vaccine efficacy but also contribute to broader immunological and general health. This review explores the transformative role of marine-derived substances in modern medicine, emphasizing their importance in the ongoing battle against infectious diseases.