Objective To investigate Hantavirus(HV) infection of captured rodents at Nansha ports and provide a scientific basis for the control of rodents and rodent-borne diseases. Methods During May 2013 to April 2014, surveillance of the rodent carriers was performed in 7 coastal harbors in Nansha. The rodents were collected using rat cages and clamps. Lung samples were taken for HFRS viral testing. HV genotype was analyzed using Real-time RT-PCR. Results A total of 538 rodents were captured, including 6 species Suncus murinus, Rattus norvegicus, R. tanezumi, Bandicota indica, Mus musculus, R. losea, among which S. murinus was the predominant group, accounting for 53.16% (286/538). Total of 538 samples were tested, the positive rate of HV was 2.60%(14/538). Nucleotide sequences analysis showed that the virus detected belongs to the Seoulvirus type. Conclusion The HV was carried by rodents at Nansha ports. Surveillance for hemorrhagic fever with renal syndrome among rodents and the control of rodents should be implemented.