Tobacco smoking and drinking alcohol are common substance use behaviors influenced by both genetic risk and environmental exposures. Traumatic events are highly prevalent, affecting about 70% of people in their lifetime. After trauma, it is unclear what role post-traumatic stress disorder (PTSD) symptoms play in substance use behaviors when accounting for this genetic risk. We used data from the Advancing Understanding of RecOvery afteR traumA (AURORA), which included 2973 participants recruited at emergency departments (EDs) within 72 h of a traumatic event and followed over time. We measured PTSD symptoms via PTSD Checklist for the DSM-5. Tobacco and alcohol consumption as frequency, quantity, and quantity-frequency in the past 30 days. We generated polygenic risk scores with continuous shrinkage for cross-ancestry estimation (PRS-CSx). We tested for main effects between PRS-CSx scores and interactions with PTSD using quasipoisson regression, with week 8 PTSD symptoms and month 6 substance use behaviors after the traumatic event. Tobacco PRS-CSx score increased the risk of tobacco use by 14% (95% CI: 1.01, 1.29, p = 0.03), and alcohol PRS-CSx score did not demonstrate consistent associations in the whole cohort (IRR: 1.08, 95% CI: 0.97, 1.19, p = 0.16). When stratified by ancestry group, both tobacco (IRR: 1.36, 95% CI: 1.14, 1.61, p < 0.001) and alcohol (IRR: 1.24, 95% CI: 1.07, 1.44, p = 0.005) PRS-CSx scores were associated with their respective outcomes in the European ancestry subcohort. Participants with lower genetic risk had stronger associations between re-experiencing symptoms and tobacco use, while participants with higher genetic risk demonstrated weaker association between re-experiencing symptoms and tobacco use. A similar pattern was observed for negative alterations in cognition/mood (NACM) symptoms-participants with lower PRS-CSx scores had stronger associations between NACM symptoms with tobacco use, compared to participants with higher PRS-CSx scores. These interactions were both statistically significant, suggesting an antagonistic effect between PRS-CSx scores and PTSD symptoms on tobacco use.