The objective of the current work was to evaluate whether the effects of acute aerobic exercise on motor learning were dependent on genetic variants impacting brain-derived neurotrophic factor (BDNF val66met polymorphism) and the dopamine D2 receptor (DRD2/ANKK1 glu713lys polymorphism) in humans. A retrospective analysis was performed to determine whether these polymorphisms influence data from our two previous studies, which both demonstrated that a single bout of aerobic exercise prior to motor practice enhanced implicit motor learning. Here, our main finding was that the effect of acute aerobic exercise on motor learning was dependent on DRD2/ANKK1 genotype. Motor learning was enhanced when aerobic exercise was performed prior to skill practice in glu/glu homozygotes, but not lys allele carriers. In contrast, the BDNF val66met polymorphism did not impact the exercise effect. The results suggest that the dopamine D2 receptor may be involved in acute aerobic exercise effects on motor learning. Such genetic information could inform the development of individualized aerobic exercise strategies to promote motor learning.