The abundances of molecules containing more than one rare isotope have been applied broadly to determine formation temperatures of natural materials. These applications of "clumped" isotopes rely on the assumption that isotope-exchange equilibrium is reached, or at least approached, during the formation of those materials. In a closed-system terrarium experiment, we demonstrate that biological oxygen (O-2) cycling drives the clumped-isotope composition of O-2 away from isotopic equilibrium. Our model of the system suggests that unique biological signatures are present in clumped isotopes of O-2-and not formation temperatures. Photosynthetic O-2 is depleted in (OO)-O-18-O-18 and (OO)-O-17-O-18 relative to a stochastic distribution of isotopes, unlike at equilibrium, where heavy-isotope pairs are enriched. Similar signatures may be widespread in nature, offering new tracers of biological and geochemical cycling.