Objective To investigate the epidemic of hemorrhagic fever with renal syndrome(HFRS) in Fujian province, China and to provide a scientific basis for the prevention and control of this disease. Methods The data on the epidemic of HFRS in 2013-2015 in Fujian province were subjected to statistical analysis. Rodents were captured using cages at night, and the population density and community structure of captured rodents was determined. Hantavirus(HV) antigen was detected and identified from rodent lungs by indirect immunofluorescence assay. Results A total of 1 309 cases of HFRS were reported in Fujian in 2013-2015, with an incidence of 1.16/100 000. The cases were widely distributed, county-level cities, or districts. The cases of HFRS were the highest in Shaowu, Jinjiang and Shishi city. The surveillance of rodents showed that the mean population density of rodents was 6.83% indoors, and Rattus norvegicus, which carried Soul virus, was the predominant species. In the mixed epidemic area,the mean population density of rodents was 5.60% in the field, and Apodemus agrarius was the predominant species. HV antigen was detected for the first time from R. norvegicus and R. tanezumi in Yunxiao, Qingliu, and Mingxi counties. Conclusion Rattus norvegicus is still the main host animal of HFRS in Fujian. The incidence of HFRS was at the highest level in 2013-2015 in Fujian, especially in Shaowu city, Songxi, Zhenghe, and Zhouning counties. Rodent control should be well performed, and HFRS bivalent vaccine should be widely used among the high-risk populations, so as to reduce the incidence and prevent the outbreak of HFRS.