The technique of larval grouper rearing has been established in Taiwan since 1985, and annual commercial seed production exceeded ten million fry in 1995. However, the larval survival rate was less than 1%, and production fluctuated due to the outbreaks of viral nervous necrosis (VNN) disease and iridovirus-like infections. In general, fertilized oysters eggs, rotifers, and copepods were sequentially applied to feed the larvae. This study was conducted to determine the benefits and disease problems associated with copepods as feed organisms. The copepods and enriched Artemia nauplii were respectively fed with the same feeding procedure. Copepods were collected from fish grow-out ponds, and were mainly Apocyclops and Pseudodiaptomus. Artemia nauplii were enriched with commercial emulsions (DC DHA Selco). Copepods contained high levels of n-3 unsaturated fatty acids (26.3 mg/g dry wt.), EPA (10.1 mg/g dry wt.), and DHA (14.4 mg/g dry wt.). In contrast, enriched Artemia contained more n-6 unsaturated fatty acids (16.1 mg/g dry wt.) than EPA (3.6 mg/g dry wt.) or DHA (2.1 mg/g dry wt.). Feeding grouper fry with copepods resulted in higher survival and faster growth than feeding with enriched Artemia. However, when fry were fed copepods, the fingerlings had more disease problems with infections of Pseudorhabdosynochus and VNN, and about 40% of fingerlings died due to those infections. Therefore, using enriched Artemia as live food is a better strategy for stabilizing fry production and lowering the risk of disease outbreaks during juvenile stages.