It is widely accepted that brain derived neurotrophic factor (BDNF) is involved in modulating behavioral performance in response to environmental conditions. The BDNF gene has been intensively studied; however, no studies have addressed the effect of BDNF gene polymorphisms on behavioral traits in sika deer (Cervus nippon). This study investigated the relationship between single nucleotide polymorphisms (SNPs) in the BDNF gene and behavior traits of sika deer in a semi-housed environment. This study was performed on Ping-Shan-Tang farm (25 deer) and in Zhu-Yu-Wan Park (23 deer), Yangzhou, Jiangsu province, China. The deer on Ping-Shan-Tang farm were housed in four 20×10 m paddocks with shelters of mantle. In Zhu-Yu-Wan Park, the deer roamed in a fenced paddock of grasses, shrubs and trees (120 m × 80 m). All deer were marked by ear-notches and collar-tags for easy identification and were aged between 3 and 7 years. Observations were conducted at the same time each day between 08:30 a.m to 16:30 p.m and deer were sampled in a different order each day (using random numbers). Each individual was studied for a mean (±S.E.) of (33.3±0.09) h and over a total of 50 weeks, 1600 h were spent observing the deer. All data were obtained with focal animal sampling and all-occurrence recording. After all observations, blood samples (10 mL) were collected from the jugular vein using vacuum tubes with acid citrate dextrose anticoagulant and then stored at -20℃. Genomic DNA was extracted from whole blood using a standard phenol/chloroform protocol, dissolved in sterile water at a concentration of 100 ng/μL and then kept at -20℃ until use. PCR amplification and SSCP analysis of the BDNF gene were performed using six pairs of primers. Two pairs of primers (P-4 and P-5) amplified polymorphic fragments. P-4 yielded a 249 bp fragment and P-5 yielded a 224 bp fragment. Three genotypes were identified by SSCP for each of the fragments amplified by the primer pairs. All behavior trait data were analyzed by one way ANOVA analysis using SPSS 14.0 software. Effects of SNPs on behavior traits were analyzed and the SNP markers that showed significant correlation with behavior traits were further studied through post-hoc multiple comparison. The results showed that: (1) The AA genotype of the P-4 fragment, had significantly greater effects on relaxaing behavior compared to the BB genotype (P<0.05), and had highly significant effects on moving behavior (P=0.001). (2) Highly significant differences in observing behavior were produced among the CC, DD and CD genotypes of the primer P-5 fragment. Also we found a highly significant difference between the CC and DD genotypes with respect to relaxing behavior (P<0.05). The same results were found on the grooming behavior (P<0.05). We conclude that polymorphisms in the BDNF gene may be involved in some aspects of behavioral traits in sika deer.