To gain more insights into the epidemiology of hantaviruses in the Guizhou province, China, rodents were captured in Guizhou during the period from 2001 to 2003. In addition, serum sample was collected from one patient. Virus isolation was attempted from human serum and rodent samples. Four hantaviruses were isolated successfully in cell culture from one human, two A. agrarius, and one R. norvegicus. The nucleotide sequences for the entire S and M and partial L segment were determined from these four isolates as well as six viruses isolated in 1980s. Phylogenetic analysis revealed that the S segment from all isolates belong to the Hantaan virus (HTNV) clade, regardless of the sources from which they were derived. According to the S sequences, these viruses could be divided into three distinct phylogroups, showing geographical clustering. Analysis of the entire M and the partial L segment sequences demonstrated that 8 out of the 10 isolates belong to the HTNV clade. However, two isolates (CGRn8316 and CGRn9415) isolated from R. norvegicus belong to the Seoul virus (SEOV) clade. In addition, these two isolates were distinct from other known members of SEOV clade. Together, the data suggest that at least three groups of HTNV are co-circulating and one new variant of SEOV may be present in Guizhou. Our results also suggest that HTNV from A. agrarius spilled over to R. norvegicus and natural reassortment between HTNV and SEOV occurred during or after the spillover.