During the last few decades, aquaculture as a useful animal protein providing sector intensifies to meet the growing world population demands. Although fish culture technological advancement has resulted in increased production, intensive technology has negatively affected the environment—consequently, aquaculture research efforts have been diverted towards developing sustainable culture technology. Introducing algae and bacteria singly or in combination in aquaculture was advantageous both by ex-vivo and in-vivo culture techniques. Utilization of microbial consortium in aquaculture can help to construct three pillars (social, economical, and ecological) of sustainability by improving water quality, reducing dependency on a wild fish stock as a feed ingredient, improving the health status of animals, and increasing economic returns along with protection of the environment. Numerous fruitful research outcomes on using algal-bacterial systems are available for its application in aquaculture. In this context, the present article highlights an updated review of current research trends on various aspects such as application of algal-bacterial consortia for aquaculture, available technologies based on their interaction, and recommendations for further improvement. This review will also provide some critical clues for the standardization of novel fish culture techniques based on microbial interaction.