Objective To determine the infection rate of hantavirus in rodents and provide basic data for the prevention and control of hemorrhagic fever with renal syndrome(HFRS) at China-Kazakhstan border railway extension line area. Methods Night trapping and arch clamp methods were applied to monitor population structure of rodents at China-Kazakhstan border railway extension line area, 95 mice's lung tissues were randomly selected to extract the RNA, and corresponding cDNA was synthesized by reverse transcription. All of 95 samples were detected by PCR targeting hantavirus. The amplified products were sequenced and analyzed. A phylogenetic tree was constructed using MEGA 6.0 software. Results Twenty-four (11 Rhombomys opimus, 4 Meriones libycus, 4 M. meridianus, 4 M. tamariscinus, 1 Cricetulus migratorius) samples were positive (24/95, 25.26%) for hantavirus. DNAman alignment analysis on 24 positive sequences, indicated that there are 6 different genotypes, and the homology was 98.41%. BLAST analysis showed that six sequences exhibited 98.09% to 98.33% similarity with the corresponding sequences of Seoul virus. The phylogenetic tree revealed that the Hantavirus agents were found in rat cluster with Seoul virus DPRK08. Conclusion Hantavirus infection was found in rodents at China-Kazakhstan border railway extension line area. The prevention and control of hantavirus in rodents should be strengthened to ensure port health safety and to prevent outbreak of the HFRS epidemic in the port area.