Alcohol use disorder (AUD) is a leading risk factor of disease burden in the world. It is also commonly comorbid with over 20% of schizophrenia patients. The brain-derived neurotrophic factor (BDNF) and dopamine D3 receptor (DRD3) have been implicated in alcohol drinking behaviour. Previous genetic studies of the BDNF and DRD3 genes produced mixed findings; however, only one study investigated two BDNF genetic markers with alcohol dependence in schizophrenia patients. We investigated 15 single-nucleotide polymorphisms (SNPs) in DRD3 and four SNPs in BDNF for possible association with alcohol abuse or dependence in schizophrenia patients of European ancestry (N = 195). The patients were assessed for the occurrence of alcohol abuse or alcohol dependence using the Structured Clinical Interview for DSM-IV Axis I Disorders, Patient Edition (SCID-I/P). We found the BDNF Val66Met to be associated with alcohol dependence (p = 0.004). We also found haplotypes across BDNF to be nominally associated with alcohol dependence. Analyses of DRD3 markers and haplotypes yielded mostly negative findings. Our findings support a role of the BDNF gene in alcohol dependence in schizophrenia patients. Larger samples are required to confirm our findings, particularly those of BDNF haplotypes.