Structured phospholipids with conjugated linolenic acid were produced for potential applications in nutraceuticals and functional foods. Structured phospholipids were synthesized with conjugated linolenic acid (CLnA) from natural sources by catalytic enzymatic reaction. Pomegranate seed oil, as a natural source of CLnA, and an isomerized-concentrated mixture (ICM) of CLnA from flaxseed oil were used for the enzymatic reaction with phosphotidylcholine (PC) using Liposyme TL IM for fatty acid modification at 57 °C for 96 h. The enzymatic process was an effective way to produce structured phospholipids with CLnA. The maximum incorporation of CLnA from pomegranate seed oil and ICM from flaxseed oil into PC was 11.3% and 4.9% after 72 h, respectively. Structured lysophospholipids were also obtained as a result of the enzymatic reaction. The maximum incorporation of CLnA from pomegranate oil and ICM from flaxseed oil into lysophospholipids was 17.2% and 13.5% after 72h, respectively. Physical properties such as dropping point and viscosity at 40 and 50 °C of the structured phospholipids produced were measured when they were added to a chocolate mixture.