This study investigated whether somatic markers mediate the effect of serotonin transporter genotype on Iowa Gambling Task (IGT) performance. Participants (N = 135) were genotyped for the insertion/deletion and single-nucleotide (rs25531) polymorphisms in the promoter region of the serotonin transporter gene (5-HTTLPR). The results of mediation analyses indicated that skin conductance responses that anticipated IGT card selections partially (i.e. 42% of the total effect) mediated the effect of genotype on IGT performance. In comparison with high-functioning 5-HTTLPR genotypes, the low-functioning genotypes were associated with higher total IGT scores. This suggests that the higher synaptic availability of serotonin, associated with the low-functioning 5-HTTLPR genotypes, may confer differential susceptibility to decision making under risk, and that almost half of this effect is explained by facilitated somatic markers during IGT.