The growth of the global population has driven the development of aquaculture as an alternative means of meeting the increasing demand for food. However, this sector faces challenges from pathogen transmission, which can impact both cultured organisms and consumers. Probiotics offer a promising solution by leveraging the antibacterial activity of certain microorganisms against pathogens. Given the limited research on the probiotic potential of microorganisms associated with marine algae, this study aimed to evaluate this potential of bacteria isolated from Bostrychia calliptera and Rhizoclonium riparium, algae from mangroves on the Pacific coast of Colombia. The antibacterial activity of the isolates was evaluated against six fish and shellfish pathogens, leading to the selection of four strains (Bacillus sp. AB08, Bacillus sp. AB17, Bacillus sp. AN35, and Pseudomonas mosselii AR37) as probiotic candidates due to their outstanding inhibition of Staphylococcus aureus. None of the selected strains formed biofilms, a favorable result from a pathogenicity perspective, while Bacillus sp. AB08 and AN35 demonstrated notable susceptibility to all tested antibiotics. Additionally, these two strains exhibited broad tolerance to temperature and pH, maintaining viable counts above 106 CFU/mL, characteristics that position them as promising candidates for use as probiotics. However, further in vitro studies are needed to better define their probiotic properties, along with in vivo evaluations in aquaculture systems to confirm their efficacy and safety.