With the intensification of aquaculture to meet the rising demands of fish and shellfish, disease outbreaks during the larval and adult stages are a major challenge faced by aqua culturists. As the prophylactic use of vaccines and antibiotics has several limitations, research is now focused on sustainable alternatives to vaccines and antibiotics, e.g., medicinal plants, probiotics, postbiotics, prebiotics, and synbiotics, as promising candidates to strengthen the immune response of fish and shellfish and to control disease outbreaks. With respect to probiotics, numerous studies are available revealing their health-promoting and beneficial impacts in aquaculture. However, most studies focus on Bacillus and Lactobacillus species. Keeping in view the positive effects of probiotic lactic acid bacteria in aquaculture, researchers are now looking for other probiotic bacteria that can be used in aquaculture. Recently, many non-lactic acid bacteria (non-LAB), which are mainly host-associated, have been reported to reveal beneficial effects in fish and shellfish aquaculture. The main non-LAB probiotic genera are Bifidobacterium, Clostridium, Microbacterium, Micrococcus, Paenibacillus, Acinetobacter, Alcaligenes, Enterobacter, Phaeobacter Pseudoalteromonas, Pseudomonas, Pseudomonas, and Vibrio. Despite the promising effects of non-LAB probiotics, comparably, there is limited available information in this context. This review focuses only on probiotic strains that are non-LAB, mostly isolated from the host digestive tract or rearing water, and discusses their beneficial effects in fish and shellfish aquaculture. This review will provide detailed information on the use of various non-LAB bacteria and provide a roadmap to future studies on new probiotics for sustainable aquaculture.