Background Alcohol Dependence (AD) and Major Depression (MD) are leading causes of disability, and they often co-occur. Genetic epidemiologic data have shown that they share, at least to some extent, a common genetic etiology. The molecular nature of this shared genetic basis is poorly understood. To detect genetic risk variants for comorbid AD and MD and to determine whether polygenic risk alleles are shared with neuropsychiatric traits or subcortical brain volumes. Methods This Genome-Wide Association Study (GWAS) analyzed criterion counts of comorbid AD and MD in data sets of African Americans (AA) and European Americans (EA) that were collected as part of the Yale-Penn study of the genetics of drug and alcohol dependence from 2000–2013. After excluding subjects who were never exposed to alcohol or had missing information for any diagnostic criterion, we performed GWAS on two samples (“Yale-Penn-1” and “Yale-Penn-2”) totaling 4,653 AAs and 3,169 EAs. AAs and EAs were analyzed separately. We then tested whether Polygenic Risk Scores (PRS) derived from potentially related traits in EAs could be used to predict comorbid AD and MD. Comorbid criterion counts (ranging from 0–14) comprised for DSM-IV AD (7 criteria) and MD (9 criteria, scaled to 7). Results Of the 7,882 participants, 42.7% were female. The median comorbid criterion count was 6.2 (interquartile range [IQR], 2.3–10.9). Under the linear regression model, rs139438618 at the Semaphorin 3A (SEMA3A) locus was significantly associated with AD-MD comorbidity in AAs in the Yale-Penn-1 sample (beta coefficient [β]=0.89, P=2.76×10-8). In the Yale-Penn-2 sample, the association was also significant (β=0.83, P=2.06×10-4). Meta-analysis of the two samples yielded a more robust association (β=0.87 [95% CI, 0.61–1.12], P=2.41×10–11). There was no significant association identified in EAs. PRS analyses showed that individuals with a higher risk of neuroticism (β=1.01 [95% CI, 0.50–1.52]) or depressive symptoms (β=0.87 [95% CI, 0.32–1.42]) and a lower level of subjective well-being (β=-0.94 [95% CI, -1.46 to -0.42]) and educational attainment (β=-1.00 [95% CI, -1.57 to -0.44]) were at higher level of AD+MD; while larger intracranial (β=1.07 [95% CI, 0.50–1.64]) and smaller putamen volumes (β=-1.16 [95% CI, -1.86 to -0.46]) predicted higher risks of AD+MD. Discussion SEMA3A variation is significantly associated with comorbid AD and MD in AAs. Using PRS analyses, we identified pleiotropy with neuropsychiatric traits and brain volumes. Further studies are warranted to understand the biological and genetic mechanisms of this comorbidity, which could facilitate medications development and other treatments for comorbid AD and MD.