We demonstrate that lipidomics coupled with molecular dynamics reveal unique phospholipase A(2) specificity toward membrane phospholipid substrates. We discovered unexpected headgroup and acyl-chain specificity for three major human phospholipases A(2). The differences between each enzyme's specificity, coupled with molecular dynamics-based structural and binding studies, revealed unique binding sites and interfacial surface binding moieties for each enzyme that explain the observed specificity at a hitherto inaccessible structural level. Surprisingly, we discovered that a unique hydrophobic binding site for the cleaved fatty acid dominates each enzyme's specificity rather than its catalytic residues and polar headgroup binding site. Molecular dynamics simulations revealed the optimal phospholipid binding mode leading to a detailed understanding of the preference of cytosolic phospholipase A(2) for cleavage of proinflammatory arachidonic acid, calcium-independent phospholipase A(2), which is involved in membrane remodeling for cleavage of linoleic acid and for antibacterial secreted phospholipase A(2) favoring linoleic acid, saturated fatty acids, and phosphatidylglycerol.