AbstractFish oil is the major dietary source of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Adequate dietary intake of these n‐3 PUFA is beneficial to reduce the risks of cardiovascular mortality, prostate cancer, and neurological disorders in children and adults. There is a surge in demand for fish oil in the functional food market. Microencapsulation of fish oil is the trend to improve its stability and sensory quality. The EPA and DHA content of the fish oil products may vary markedly from the label due to their susceptibility to oxidation. Quick and reliable methods other than the AOAC BF3 method have been exploited to quantify EPA and DHA in the encapsulated fish oil and the microencapsulated powdered products such as infant formula. This article describes a method to differentiate the ethyl‐ester form from the TAG form of EPA and DHA in encapsulated fish oil which may be a mixture of natural triacylglycerol enriched with ethyl esterified EPA and DHA. A method is recommended due to the difference in apparent potency of these two esterified forms, which may be a concern in infant formula and elsewhere.