Aims To investigate whether the effects of family conflict on adolescent drinking differed as a function of 5-HTTLPR genotype cross-sectionally and prospectively in two independent samples of adolescents. Design Path analysis and multi-group analysis of two prospective datasets were conducted.Settings United States and United Kingdom.Participants Sample 1 was 175 adolescents in the U.S. (mean age = 15 at Times 1 and 2 with a six-month interval); Sample 2 was 4,916 adolescents in the U.K. (mean age = 12 at Time 1 and 15 at Time 2).Measurements In both samples, demographics, tri-allelic 5-HTTLPR genotype, and perceived family conflict were assessed at Time 1.; Alcohol use (frequency of drinking), and alcohol misuse (frequency of intoxication, frequency of drinking 3 or more drinks, maximum number of drinks) were assessed at Times 1 and 2.FindingsA significant gene-environment interaction on alcohol misuse at Time 1 was found in both Sample 1 (β = .57, p = .001) and Sample 2 (β = .19, p = .01), indicating that the 5-HTTLPR low-activity allele carriers exposed to higher levels of family conflict were more likely to engage in alcohol misuse than non-carriers. A significant gene-environment interaction effect on change in alcohol misuse over time was found only in Sample 1 (β = .49, p = .04) but not in Sample 2 (β = .02−.08, p = .19−.70).Conclusions Compared with non-carriers, adolescents carrying the 5-HTTLPR low-activity allele are more susceptible to the effects of family conflict on alcohol misuse.