One H6N6 subtype avian influenza virus 〔A/environment/Zhenjiang/zj18/2013 (en/zj18)〕 was isolated from a live poultry market in Zhenjiang in an epidemiological surveillance and was subjected to genome sequencing and further analysis. Next-generation sequencing (NGS) by Illumina MiSeq Platform was used to obtain the complete genome sequence from the isolated virus. MEGA5.0 software was used to align the eight fragments respectively. The phylogenetic and molecular characteristics of the isolate were analyzed by Neighbor-Joining method. BLAST searches demonstrated that the 8 genes (PB2, PB1, PA, HA, NP, NA, M and NS) had 96.7%－99.6% nucleotide identity with the ones on the H6N6 subtype reference viruses circulating in southeast China. The enzyme cleavage site on HA was PQIETR↓GL, which was the typical characteristic of the low pathogenic avian influenza virus (LPAIV). The key HA receptor binding sites were E190 and G228, indicating a preference binding for α2-3-linked sialic acids. The results suggest that it is necessary to strengthen the continuous surveillance of avian influenza A viruses.