Introduction: Brain-derived neurotrophic factors (BDNF) play a role on induction and maintenance of memory and learning. The BDNF gene Val66Met polymorphism impairs expression of this protein. Due to difference between the neural principles operating during motor memory consolidation and the neural principles operating during practice (acquisition) and the effect of BDNF on both of these processes, the aim of the study was to study the effect of val66met polymorphism on acquisition and motor memory consolidation in the process of learning of throwing motor skill. Materials and Methods: We randomly selected one hundred university students of Kashan , Iran (mean age: 21.6±2.2 years). After blood sampling, extraction of genomic DNA, implementation of polymerase chain reaction, analyzing of PCR by 1.5 percent Electrophoresis Gel, and in the end sequencing by ABI PRISM 7000 Sequencing Analyzer, 46 participants were identified without val66met polymorphism, and 54 participants identified affected by the polymorphism (met-carriers). 10 participants of each genetic group (20 people) after pre-test practiced backhand baseball pitch for six sessions. After 48 and 96 hours they participated in two consecutive retention tests. Results: Our data showed no difference between met-carriers and people without the polymorphism in acquisition and the first retention test. However, met-carriers were significantly weaker than people without the polymorphism in the second retention test. Conclusion: These findings suggest that the BDNF val66met polymorphism has higher impact on motor learning in the consolidation phase than acquisition phase.