A 28-day feeding experiment with formulated feed using docosahexaenoic acid (DHA)-rich whole cells of freeze-dried marine microalgae Schizochytrium sp. to understand the distribution of fatty acids in a laboratory model zebrafish was conducted. Three feeds, commercial feed, 50:50 feed (50% commercial and 50% algae), and pure algae, were investigated. All feeds were consumed by zebrafish and showed optimal growth and weight gain with a survival rate of 100%. Lipids were extracted from four different tissues, brain, liver, muscle, and blood, to understand the distribution of fatty acids with respect to the feed. Maximum lipid was observed in zebrafish fed with 50:50 feed in all tissue samples. An increasing concentration of fatty acids was observed upon increasing the experimental time. Algae feed supported the DHA accumulation in all tissue samples compared to other feeds and resulted in an overall increment of polyunsaturated fatty acid content. To understand the role of fatty acids during zebrafish embryogenesis, eggs were collected at the end of the experiment and fatty acid content was analyzed. However, no significant difference was observed in fatty acid composition of embryos fed with algae. This provides a base for the understanding of fatty acid distribution in zebrafish with commercial and algae feeds and support the utilization of Schizochytrium biomass as a potential replacement for fishmeal.