The emerging aquaculture industry is in need of non-antibiotic-based disease control approaches to minimize the risk of antibiotic-resistant bacteria. Bacterial infections mainly caused by Vibrio spp. have caused mass mortalities of fish especially during the larval stages. The objectives of this study were to verify the potential of symbiotic probiont strains, isolated from microalgae (Amphora, Chlorella, and Spirulina) for suppressing the growth of Vibrio spp. and at the same time ascertain their abilities to enhance microalgal biomass by mutualistic interactions through microalgae-bacteria symbiosis. In addition, in vivo studies on Artemia bioencapsulated with probiont strains (single strain and mix strains) and microalgae were evaluated. The selected potential probionts were identified as Lysinibacillus fusiformis strain A-1 (LFA-1), Bacillus sp. strain A-2 (BA-2), Lysinibacillus fusiformis strain Cl-3 (LFCl-3), and Bacillus pocheonensis strain S-2 (BPS-2) using 16s rRNA. The cell densities of Amphora culture supplemented with BA-2 and Chlorella culture supplemented with LFCl-3 were higher than those of the controls. Artemia bioencapsulated with mix strains (LFA-1 + BA-2 + LFCl-3 + BPS-2) and Amphora demonstrated the highest survival rate compared to the controls, after being challenged with V. harveyi (60 ± 4%) and V. parahaemolyticus (78 ± 2%). Our study postulated that BA-2 and LFCl-3 were found to be good promoting bacteria for microalgal growth and microalgae serve as a vector to transport probiotic into Artemia. Moreover, mixture of potential probionts is beneficial for Artemia supplementation in conferring protection to Artemia nauplii against pathogenic Vibrios.