When individuals are exposed to stressful environmental challenges, the response varies widely in one or more of three components: psychology, behavior and physiology. This variability among individuals can be defined as temperament. In recent years, an increasing large body of evidence suggests that the dimensions of temperament, as well as personality, psychological disorders and behavioral traits, are influenced by genetic factors, and much of the variation appears to involve variation in genes or gene polymorphisms in the hypothalamic–pituitary–adrenocortical (HPA) axis and the behavior-controlling neurotransmitter networks. Here, we review our current understanding of the probabilistic impact of a number of candidate gene polymorphisms that control temperament, psychological disorders and behavioral traits in animals and human, including the gene polymorphisms related to corticotrophin-releasing hormone (CRH) production and adrenal cortisol production involved in the HPA axis, and a large number of gene polymorphisms in the dopaminergic and serotonergic neurotransmitter networks. It will very likely to assist in diagnosis and treatment of human relevant disorders, and provide useful contributions to our understanding of evolution, welfare and conservation, for animals in the wild and in production systems. Additionally, investigations of gene–gene and gene–environment complex interactions in humans and animals need further clear illustration.