Rodents are the major natural reservoir of hantaviruses, which cause two main human zoonoses, haemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome (HPS) in the Americas. Surveillance of hantaviruses in rodents plays an important role in the prevention and control of HFRS and HPS. In this study, small mammals were captured in an HFRS-endemic region, Luxi County within the Yunnan Province of China, from the autumn of 2009 to the spring of 2010, and assessed for the presence of hantaviruses. A high ratio of hantavirus infection was detected in the Yunnan red-backed vole (Eothenomys miletus). Full-length sequences of the small, middle and large segments were determined from one positive sample (designated Luxi hantavirus). Analyses of the coding sequences indicated that this virus represents a distinct hantavirus species within the hantavirus group identified from the Rodentia subfamily Arvicolinae.