Corticolimbic pathways connecting the amygdala and ventral prefrontal cortex (vPFC) are linked with trait anxiety, but it remains unclear what potential genetic moderators contribute to this association. We sought to address this by examining the inter-individual variability in neuroplasticity as modeled by a functional polymorphism (rs6265) in the human gene for brain derived neurotrophic factor (BDNF). Amygdala-vPFC pathway fractional anisotropy (FA) from 669 diffusion magnetic resonance images was used to examine associations with trait anxiety as a function of rs6265 genotype. We first replicated the inverse correlation between trait anxiety and amygdala-vPFC pathway FA in women. Furthermore, we found a moderating influence of rs6265 genotype such that the association between trait anxiety and right amygdala-vPFC pathway FA was strongest in women carrying the Met allele, which is linked with decreased activity-dependent neuroplasticity. Results indicate that the microstructural integrity of pathways supporting communication between the amygdala and vPFC help shape the expression of trait anxiety in women, and that this association is further modulated by genetically driven variability in neuroplasticity.