To gain more insights into hantavirus distribution in China, Microtus fortis were caught in Jilin province and M. maximowiczii in the Inner Mongolia Autonomous Region. Hantavirus specific RNA was detected by RT-PCR in 3 out of 26 M. fortis and 5 out of 64 M. maximowiczii. Two hantaviruses (Fusong-Mf-682 and Yakeshi-Mm-59) were isolated successfully in cell culture and their S and M segment nucleotide sequences were determined. Phylogenetic analysis of the S and M segment sequences revealed that the Mf-originated strains from Fusong were closely related to Vladivostok hantavirus (VLAV) with 99% nucleotide identity, but differed from the Yakeshi-Mm strains, with an amino acid divergence of more than 8.8% for the N protein and 11.8% for the GnGc proteins. Yakeshi-Mm strains were closely related to the Khabarovsk hantavirus (KHAV) isolated earlier from M. fortis in Khabarovsk, with an amino acid sequence identity of more than 98.4% for the S segment and 95.6% for the M segment. On phylogenetic trees, Yakeshi-Mm strains clustered together with KHAV and Topografov virus (TOPV) carried by Lemmus sibiricus. The results suggest that the hantavirus carried by M. fortis in China belongs to VLAV type and should be considered as a distinct hantavirus species. They also suggest that M. fortis is the natural host of VLAV (including Fusong-Mf strains), whereas M. maximowiczii is the natural host of KHAV including Yakeshi-Mm strains. Thus, in addition to Hantaan, Seoul, Dabieshan and Puumala-like Hokkaido viruses, at least two other hantaviruses, namely KHAV and VLAV, are circulating in China.