Hantaan (HTN) and Seoul (SEO) viruses, murid rodent-borne hantaviruses, are known to causes hemorrhagic fever with renal syndrome (HFRS) in Korea. To determine the genomic diversity and molecular phylogeny of HTN and SEO viruses found in Korea, we amplified for part of M and S genomic segments of hantaviruses from sera of HFRS patients and lung tissues of hantavirus seropositive striped-field mice. Both M and S segment of 16 HTN and 2 SEO viruses were amplified by nested reverse transcripton-polymerase chain reaction. Based on 324 nucleotides in the M genomic segment, the HTN and SEO strains showed 93.8~100% and 99.1~99.4% homologies, respectively. Similarly, based on 230 nucleotides in the S genomic segment, HTN and SEO strains showed 90.9~100% and 100% homologies, respectively. Phylogenetic analysis of M and S segments indicated that HTN strains could be divided into at least two main groups in M and S trees and the sequence differences detected among the S and M genomic segments of HTN viruses are consistent with reassortment having taken place between HTN virus strains.