To provide a better understanding of hantavirus epidemiology in China, Korean field mice (Apodemus peninsulae) and striped field mice (Apodemus agrarius) were captured in Jilin province, China, where haemorrhagic fever with renal syndrome (HFRS) is endemic. Hantavirus antigens were detected in eight of the 130 A. peninsulae individuals and in four of the 193 A. agrarius individuals by using an immunofluorescence assay. Partial S and M segments were amplified from all of the antigen-positive samples. Furthermore, two hantaviruses (CJAp89 and CJAp93) were isolated successfully in cell culture and the entire S and M segments were amplified from one of them (CJAp93). Phylogenetic analysis of these sequences (partial or complete) showed that hantaviruses carried by A. peninsulae and A. agrarius form two distinct lineages, although viruses carried by A. peninsulae are similar to those isolated previously from A. agrarius in China and from HFRS patients in Russia. However, the viruses detected in A. peninsulae in China are genetically different from those detected in A. peninsulae in other countries. These data suggest that A. peninsulae is also a natural host for HTNV in north-eastern China.