A major constraint in successful larviculture of groupers has been the small gape of the larvae and hence the requirement for small prey at first feeding. In this study, we examined how maintaining a phosphate concentration of 100 μg P L−1 and an inorganic nitrogen (N) level of 700 μg N L−1 via weekly fertilization with inorganic fertilizers affected phytoplankton, zooplankton and giant grouper larval survival in relation to a control group that was provided with rotifers immediately after larvae hatched. Unicellular algae, zooplankton within the size ranges of 10–50 μm and 50–100 μm and survival of giant grouper larvae were all significantly higher in the fertilized treatment compared with the control. Stomach analysis revealed that ciliates and flagellates were actively consumed by larval fish in the fertilized group, whereas few rotifers were consumed in the control. We conclude that the inorganic fertilization method provides high densities of suitable-sized prey for larval groupers at the onset of exogenous feeding before they are able to consume larger, commercially available rotifers and copepods.