Dual process models of addiction emphasize the importance of implicit (automatic) cognitive processes in the development and maintenance of substance use behavior. Although genetic influences are presumed to be relevant for dual process models, few studies have evaluated this possibility. The current study examined two polymorphisms with functional significance for alcohol use behavior (COMT Val158Met and ALDH2*2) in relation to automatic alcohol cognitions and tested additive and interactive effects of genotype and implicit cognitions on drinking behavior. Participants were college students (n = 69) who completed Implicit Association Tasks (IATs) designed to assess two classes of automatic drinking motives (enhancement motives and coping motives). Genetic factors did not show direct associations with IAT measures; however, COMT and ALDH2 moderated associations of implicit coping motives with drinking outcomes. Interaction effects indicated that associations of implicit motives with drinking outcomes were strongest in the context of genetic variants associated with relatively higher risk for alcohol use (COMT Met and ALDH2*1). Associations of genotype with drinking behavior were observed for ALDH2 but not COMT. These findings are consistent with the possibility that genetic risk or protective factors could potentiate or mitigate the influence of reflexive cognitive processes on drinking behavior, providing support for the evaluation of genetic influences in the context of dual process models of addiction.