Genetic approaches to both the gender-science stereotype and implicit social cognition have received increasing attention in recent years. We explored whether single nucleotide polymorphisms (SNPs) in dopaminergic and neurotrophic systems (i.e., COMT, BDNF genotypes) explain variations in the implicit gender-science stereotype. We genotyped 413 adolescents and assessed their implicit gender-science stereotype with the Implicit Association Test. Replication on a subsample (N = 312) was conducted 2 years later. Results showed that SNP-level variations within the COMT and BDNF genes were consistently associated with the implicit gender-science stereotype in both investigations. These findings suggest that variants in the COMT and BDNF genes may contribute to the variation of implicit gender-science stereotype.