In order to understand the distribution and prevent the prevalence of subtype avian influenza virus of H6, surveillance for H6 virus was implemented in the wholesale markets of live poultry and waterfowl fields around the Dongting Lake. Samples were firstly injected to embryos of SPF chicken by allantoic cavity, and then the allantoic fluid was collected and tested using hemagglutination (HA). If a positive result was gotten, then subtypes of the virus would be determined by hemoagglutination inhibition (HI) and RT–PCT. The surveillance demonstrated that H6 virus was isolated from chickens, ducks and geese sampled at all wholesale markets of live poultry with a total separation rate of 6.49%. The positive rate of subtype virus of H6 in the waterfowl fields was 3.6%, and the separation rate from swabs was 0.29%, while, the separation rate from duck swabs was 9.58% in the wholesale markets of live poultry. These results indicated that the hidden risk of H6 virus in the wholesale markets of live poultry was higher than that of in waterfowl fields.