It is widely accepted that brain-derived neurotrophic factor (BDNF) is involved in modulating behaviour performance induced by environmental conditions. The aim of this study was to study polymorphisms of the BDNF gene and their relationship with animal behaviour in sika deer (Cervus nippon). Forty-eight sika deer reared at the Ping-Shan-Tang Farm (25 deer) and Zhu-Yu-Wan Park (23 deer), Yangzhou City, Jiangsu Province (China) were observed and blood samples were taken to identify BDNF genotypes. Data were subjected to ANOVA analysis to evaluate the link between genotype and animal behaviour traits. After PCR and electrophoresis, polymorphisms were found in two pairs of primers. At primer P-4, the AA genotype (26 deer) rested significantly less than the BB genotype (16 deer) (P<0.05). The AA genotype deer also exhibited significantly more locomotor behaviour (P=0.001). At primer P-5, deer of genotypes CC/DD/CD differed significantly in their watching behaviour. Deer of genotype CC exhibited significantly less resting and self-grooming behaviour than deer of genotypes CD or DD (both P<0.05). Our findings suggest that polymorphisms in BDNF may be involved in some aspects of animal behaviour traits, especially in the highly sensitive sika deer reared for several years in Chinese parks.