Phospholipase D (PLD)-mediated transphosphatidylation of squid skin lecithin with L-serine was examined to prepare docosahexaenoic acid-containing phosphatidylserine (DHA-PS). When a biphasic system with organic solvent and 0.2 M acetate buffer (pH 5.5) was used, PS synthesis was significantly affected by the amount of 3.4 M L-serine-containing acetate buffer. L-Serine concentration in the acetate buffer and choice of organic solvent were also crucial. In a typical reaction with 0.8 unit of PLD (Streptomyces sp.), 2.5 mL of ethyl acetate substrate solution containing 30 mg of squid skin lecithin in combination with 3 mL of 3.4 M L-serine-containing 0.2 M acetate buffer (pH 5.5), PS content in the recovered phospholipid fraction increased to 43.1% after 24 h. DHA composed 37.6% of fatty acids in the converted PS. This was the same DHA level as in the substrate. Phosphatidylcholine (squid skin PC, DHA 44.2%) in the squid skin lecithin was more effectively converted to PS than phosphatidylethanolamine.