Feral horses (Equus caballus) have a complex social structure, the stability of which is important to their overall health. Behavioral and demographic research has shown that decreases in group (or band) stability reduce female fitness, but the potential effects on the physiological stress response have not been demonstrated. To fully understand how band stability affects group-member fitness, we need to understand not only behavioral and demographic, but also physiological consequences of decreases to that stability. We studied group changes in feral mares (an activity that induces instability, including both male and female aggression) on Shackleford Banks, NC. We found that mares in the midst of changing groups exhibit increased fecal cortisol levels. In addition, mares making more group transfers show higher levels of cortisol in the two weeks following the changes. These results offer insights into how social instability is integrated into an animal's physiological phenotype. In addition, our results have important implications for feral horse management. On Shackleford Banks, mares contracepted with porcine zona pellucida (PZP) make approximately 10 times as many group changes as do untreated mares. Such animals may therefore be at higher risk of chronic stress. These results support the growing consensus that links between behavior and physiological stress must be taken into account when managing for healthy, functional populations.