This study assessed in vitro interaction betweenBacillusbacteria and microalgae and their posterior in vivo effect on rearing Kumamoto oysterCrassostrea sikamea. The probiotic strainsBacillus licheniformis(MAt32),B. subtilis(MAt43) andB. subtilis(GAtB1) were individually inoculated in triplicate into 250 mL flasks containing 1 x 10(4)colony forming units (CFU) mL(-1)of bacteria and 4.5 x 10(4)cell mL(-1)of microalgae (Isochrysis galbanaorChaetoceros calcitrans) to evaluate their growth during a 7-day culture. Single cultures of microalgae or bacilli served as control. Additionally,C. sikameaspat was treated for 28 days with four single/combined bacillus treatments in triplicate at a concentration of 1 x 10(6) CFU mL(-1)as follows: (a) control, without treatments; (b) combination of two antibiotics (10 mg L-1); (c)B. licheniformis; (d)B. subtilis; (e)B. subtilis subtilisand (f) mixed bacilli. The results showed a significantly (P < 0.05) increased growth ofBacillusstrains co-cultured with microalgae, while the growth ofI. galbanaco-cultured with bacteria was not reduced significantly (P > 0.05) compared with the control group.C. sikameaspat treated withBacillusshowed significantly (P < 0.05) higher growth and survival than the control group. In this study,C. calcitransmicroalgae were susceptible to the presence of probiotic bacteria. Nonetheless, this reduction in microalgal growth observed in vitro increased growth and survival ofC. sikameaspat exposed to probiotic bacteria when compared to spat without probiotics.