As shown by clinical genetic studies, affective and anxiety disorders are complex genetic disorders with genetic and environmental factors interactively determining their respective pathomechanism. Advances in molecular genetic techniques including linkage studies, association studies, and genome-wide association studies allow for the detailed dissection of the genetic influence on the development of these disorders. Besides the molecular genetic investigation of categorical entities according to standardized diagnostic criteria, intermediate phenotypes comprising neurobiological or neuropsychological traits (e.g., neuronal correlates of emotional processing) that are linked to the disease of interest and that are heritable, have been proposed to be closer to the underlying genotype than the overall disease phenotype. These intermediate phenotypes are dimensional and more precisely defined than the categorical disease phenotype, and therefore have attracted much interest in the genetic investigation of affective and anxiety disorders. Given the complex genetic nature of affective and anxiety disorders with an interaction of multiple risk genes and environmental influences, the interplay of genetic factors with environmental factors is investigated by means of gene-environment interaction (GxE) studies. Pharmacogenetic studies aid in the dissection of the genetically influenced heterogeneity of psychotropic drug response and may contribute to the development of a more individualized treatment of affective and anxiety disorders. Finally, there is some evidence for genetic factors potentially shared between affective and anxiety disorders pointing to a possible overlapping phenotype between anxiety disorders and depression.