Brief physical exercise enhances memories for neutral events, and modulates fear learning in animals. Exercise-induced arousal induces the release of brain-derived neurotrophic factor (BDNF), which may moderate memory-enhancing effects. This study investigated the effect of exercise, and the extent to which the BDNF val66met polymorphism (which limits BDNF activity-dependent secretion) influenced emotional memories. Sixty-two healthy participants were randomly assigned to either 10min of intense exercise (n=31) or slow walking (control condition; n=31), and then immediately viewed positive and negative images. Saliva samples were collected to index salivary cortisol, and to determine BDNF val66met genotype. Participants completed memory questionnaires two days later. Participants in the exercise had a significant increase in cortisol, and recalled more emotional images relative to the walking condition. Regression analyses indicated that the interaction between the BDNF val/val allele and cortisol response predicted stronger emotional memory in the exercise condition. These findings are consistent with evidence of acute exercise-induced emotional learning in animals, and suggests that a genetic predisposition involving BDNF may be important in determining the impact of acute exercise on emotional memory formation.