Algae and bacteria are both the oldest forms of life on our planet, and billions of years of natural evolution have driven the algae and their microbiomes to evolve into interactive phycobionts. Through complex, flexible, intelligent, and multi-interface interactions between algae and bacteria, the functions of both sides of the phycobionts are exquisitely regulated. The creation, innovation, and development of the phycobiont theory shows vital scientific value for revealing the mystery of the origin and evolution of the life on Earth, and this theory is also being transformed into diverse practical applications in significant fields for sustainable development. After centuries of incubation, knowledge accumulation and development, currently, it is the right time to promote Phycosphere Microbiology to develop into an emerging interdiscipline. In this review, we comprehensively discussed the core concepts of Phycosphere Microbiology, sorted out its vital relationships with environment protection, human health maintenance, resource utilization, and green-oriented transition of energy, then reviewed its development history, and summarized the main research achievements during three development periods. Finally, we also proposed and discussed the future development trends and potential research directions for this emerging interdiscipline.