Intrusive memories are a key symptom of Post-Traumatic Stress Disorder (PTSD). Brain Derived Neurotrophic Factor (BDNF) has been proposed as a possible mechanism underlying intrusive memories in PTSD given its role in synaptic plasticity and memory consolidation. The BDNF Val66Met polymorphism has been linked to PTSD susceptibility and memory disturbances however previous research outcomes have been variable, potentially due to a failure to control for important confounds such as sex, ethnicity, developmental stage and extent of previous trauma experiences. This study explored the relationship between the BDNF Val66Met and emotional memory (intrusive memories and recall) in PTSD controlling for these factors in 276 participants: 53 with PTSD, 118 Trauma Exposed and 105 Controls. Key findings revealed the PTSD group experienced significantly more negative intrusions than Controls, with no group differences for negative memory recall. Females reported more intrusive memories than males, however there were no sex differences in negative memory recall. When developmental stage of trauma was considered in a traumatised sub-sample, BDNF genotype significantly interacted with PTSD status, sex, and developmental trauma stage. This highlights the importance of controlling for neurobiological influences on BDNF expression, however further research is imperative to replicate these findings and investigate the specific epigenetic and neural processes involved.