Abstract: Objective To understand the predominant influenza virus strain and its variation in border area in Guangxi and provide scientific evidence for the prevention and control of influenza and human avian influenza virus. Methods In the border area, the etiological surveillance was conducted among the cases of pneumonia/severe pneumonia with unknown origin by collecting their throat swabs to extract viral nucleic acid for PCR and influenza virus isolation and identification were conducted among influenza like illness cases in the sentinel hospitals, and the blood samples were taken from the people with occupational exposure to poultry to detect antibody of avian influenza A (H5N1) by using hemagglutination inhibition test. Results A total of 6 strains of influenza viruses were isolated in 2008, including 5 strains of B virus and 1 strain of A (H1N1) virus, thirty-three strains of influenza viruses were isolated in 2009, including 17 strains of B virus, eight strains of A (H3N2) virus, two strains of A(H1N1) virus and 6 strains of pandemic A(H1N1) virus, and 130 strains of influenza viruses were isolated in 2010, including 55 strains of B virus, forty-nine strains of A (H3N2) virus, one strain of A(H1N1) virus and 25 strains of pandemic A (H1N1) virus; During 2008-2010, nine samples from the cases of pneumonia/severe pneumonia with unknown origin were detected, all the samples were negative in detection of avian influenza virus and multiplex PCR for respiratory viruses, 34 blood samples from the people with occupational exposure to poultry were detected, but no antibody of avian influenza virus was detected. Conclusion The predominant strains were influenza B virus in 2008 and 2009, influenza A (H3N2) and influenza B viruses in 2010 in border area in Guangxi. No avian influenza virus was detected in the samples from the cases of pneumonia/severe pneumonia with unknown origin and no inapparent infection of avian influenza virus was detected in people with occupational exposure to poultry It is important to strengthen the etiological surveillance of influenza and avian influenza for the prevention and control of the diseases in border area in Guangxi.