Two suspected hantavirus pulmonary syndrome (HPS) cases from Bolivia occurred in May and July 2000 and were confirmed by enzyme-linked immunosorbent assay (ELISA)-ANDES using N-Andes recombinant antigen serology. Clot RNAs from the two patients were subjected to reverse transcription-polymerase chain reaction (PCR) amplification and sequencing. We describe two characterized cases of HPS. One was caused by infection with Bermejo virus and the other with Andes Nort viral lineage, both previously obtained from Oligoryzomys species. This is the first report of molecular identification of a human hantavirus associated with Bermejo virus.