Prostaglandin H synthase isoform-1 (PGHS-1) cyclooxygenase activity has a cooperative response to arachidonate concentration, whereas the second isoform, PGHS-2, exhibits saturable kinetics. The basis for the cooperative PGHS-1 behavior and for the difference in cooperativity between the isoforms was unclear. The two cyclooxygenase activities have different efficiencies of feedback activation by hydroperoxide. To determine whether the cooperative kinetics were governed by the feedback activation characteristics, we examined the cyclooxygenase activities under conditions where feedback activation was either assisted (by exogenous peroxide) or impaired (by replacement of heme with mangano protoporphyrin IX to form MnPGHS-1 and -2). Heme replacement increased PGHS-1 cyclooxygenase cooperativity and changed PGHS-2 cyclooxygenase kinetics from saturable to cooperative. Peroxide addition decreased or abolished cyclooxygenase cooperativity in PGHS-1, MnPGHS-1, and MnPGHS-2. Kinetic simulations predicted that cyclooxygenase cooperativity depends on the hydroperoxide activator requirement and initial peroxide concentration, consistent with observed behavior. The results indicate that PGHS-1 cyclooxygenase cooperativity originates in the feedback activation kinetics and that the cooperativity difference between the isoforms can be explained by the difference in feedback activation loop efficiency. This linkage between activation efficiency and cyclooxygenase cooperativity indicates an interdependence between fatty acid and hydroperoxide levels in controlling the synthesis of potent prostanoid mediators.