Physiology has the potential to play a unique and important role in conservation and management practices by helping identify the mechanistic responses of populations to environmental changes, and providing physiological tools and knowledge that can be applied to help solve conservation and environmental problems. It has previously been unclear, however, if the increase of physiology in conservation and management literature has translated into the application of physiological tools and knowledge into conservation and management plans. There were two purposes of this disquisition: 1) analyze how physiological tools have been integrated into applied conservation by reviewing USFWS endangered species recovery plans, and provide suggestions to help conservation scientists and physiologists work synergistically to solve conservation and management problems, and; 2) provide an example of how studying the physiology of a species can provide useful information for making management decisions, using the study of stress physiology in the red-winged blackbird (Agelaius phoeniceus) during their breeding season as our case study. Our results suggest that physiology is being underutilized in USFWS endangered species recovery plans. We hypothesize this absence of physiological tools and knowledge in conservation planning is primarily due to a deficit of physiological knowledge passing between physiologists and the cohort of federal agency recovery plan writers. We suggest the need for increased training of federal agency employees, the inclusion of authors with academic affiliations, increased integration of physiology and conservation research, and enhanced communication between all concerned parties. To illustrate how physiology can be useful, we exposed female red-winged blackbirds to predator and nest parasitism effigies, thus causing additional stress, during the breeding season. We were able to examine how females respond behaviorally and physiologically to stress, and how these responses alter their reproductive decisions. We found that females are responding both behaviorally and physiologically to the increased threat of predation and nest parasitism. There is potential to exploit these responses to manage the species, such as causing females to forgo breeding. We also determined that an individual’s stress physiology can be changed when held in captivity. We suggest using caution when trying to extrapolate captive data to wild populations.