Social stress is the most common stressor experienced by humans and exposure to social stress is thought to cause or exacerbate neuropsychiatric illness. Social stress also leads to behavioral and physiological responses in many animal models that closely mirror the symptoms of fear and anxiety in humans. Our laboratory uses Syrian hamsters to study behavioral responses to social stress. Hamsters are highly territorial, but after losing an agonistic encounter, hamsters exhibit a striking behavioral change, abandoning all territorial aggression and instead becoming highly submissive. This behavioral shift is termed conditioned defeat. Epigenetic modifications, such as changes in histone acetylation, are a possible molecular mechanism underlying such behavioral shifts. Histone deacetylase (HDAC) inhibitors have been shown to enhance fear learning and conditioned place preference for drugs of abuse, while suppressing histone acetylation with histone acetyltransferase (HAT) inhibitors impairs long-term memory formation. The first goal of this study was to test the hypothesis that histone acetylation is a molecular mechanism underlying conditioned defeat. We found that animals given an HDAC inhibitor systemically before social defeat later exhibited increased conditioned defeat. This treatment also suppressed defeat-induced immediate-early gene activity in the infralimbic cortex but not the basolateral amygdala. Next, we demonstrated that administration of an HDAC inhibitor in the infralimbic cortex before defeat enhanced stress-induced behavioral responses while HAT inhibition blocked these behavioral changes. Although both males and females exhibit conditioned defeat, the behavioral expression is more pronounced in males. We next used transcriptomic analysis to investigate potential genetic mechanisms leading to this sexually dimorphic expression and to further delineate the role of acetylation in stress-induced behavioral changes. We sequenced the whole brain transcriptome of male and female hamsters as well as the transcriptome of basolateral amygdala, a nucleus necessary for the acquisition and expression of conditioned defeat, of dominant, subordinate, and control animals. Our analysis revealed that numerous genes relating to histone acetylation, including several HDACs, were differentially expressed in animals of different social status and between sexes. Together, these data support the hypotheses that histone modifications underlie behavioral responses to social stress and that some of these modifications are sexually dimorphic.