In aquaculture, Spirulina platensis is used as feed supplement in which contains amino acid phenylalanine. This study was conducted to evaluate the differences in the effect of spirulina-based microcapsules and commercial diets on the absolute, daily and specific growth and survival rates of milkfish larvae. The larvae were fed with Spirulina platensis as a core diet in microcapsules with different matrix (walls). The first capsule wall was gelatin and fish oil, while the second capsule wall was gelatin, fish oil and whole egg. The control group was fed with the commercial diet. A total of 1200 larvae were used in this experiments using the recirculation systems. The experiment was conducted in 42 days of culture. Larvae were fed three times a day and the feed was increased regularly as the size of the larvae increased. The results showed that the effects of both sprirulina-based microcapsules diets on the absolute growth rate (AG), specific growth rate (SGR) and average daily growth rate (ADGR) of Chanos chanos larvae were the same as on those larvae which were fed with the commercial diet. The survival rates were at 80.6±11.17% for those fed with Spirulina platensis with gelatin and fish oil wall; 84.6±8.44% for those fed with Spirulina platrensis with gelatin, fish oil and whole egg wall, and; 83.8±16.50% for those fed with the commercial diet. This study showed that Spirulina-based microcapsules had the same effect as the commercial feed on the growth of milkfish larvae indicating that this diet could replace the commercial diet.