The comorbidity of generalized anxiety disorders (GAD) with alcohol use disorders (AUD) is common and there is an association between the serotonin transporter (SERT) genetic variation and the comorbid conditions of GAD and AUD. However, few mechanistic studies have systematically explored the role of direct SERT manipulation in stress-elicited mood disorders. Therefore, the aim of this study was to determine whether reductions in SERT expression in the hippocampus were sufficient to ameliorate anxiety- and ethanol-related behaviors in socially defeated mice. Following stress exposure, and using stereotaxic surgery, SERT was knocked down using specific shRNA-expressing lentiviral vectors and anxiety-like behavior was evaluated by open-field, elevated plus maze, and marbles burying test. The two-bottle choice (TBC) drinking paradigm was used to assess stress-induced voluntary ethanol intake and preference. Results showed that hippocampal SERT loss-of-function prevented stress-elicited anxiogenic-like effects with no differences in spontaneous locomotor activity. Moreover, in the TBC paradigm, SERT shRNA-injected mice consistently showed a significantly decreased consumption and preference for ethanol when compared to Mock-injected controls. In contrast to ethanol, SERT shRNA-injected mice exhibited similar consumption and preference for saccharin and quinine. Interestingly, we confirmed that SERT hippocampal mRNA expression correlated with measures of anxiety- and ethanol-related behaviors by Pearson correlation analysis. Our findings show that social defeat recruits hippocampal serotoninergic system and that these neuroadaptations mediate the heightened anxiety-like behavior and voluntary alcohol intake observed following stress exposure, suggesting that this system represents a major brain stress element responsible for the negative reinforcement associated with the "dark side" of alcohol addiction.