【Objective】In order to comprehend the molecular characteristics of duck Tembusu virus , the isolations of GDNS2010.1, GDNS2010.2, GDZQ2012, GDPY2013 in the Pearl River Delta region were analyzed.【Method】 From the reference strains (GenBank accession no.JS804), eleven pairs of specific primers were designed and synthesized to amplify genome sequence fragments of GDNS2010.1, GDNS2010.2, GDZQ2012, GDPY2013. The whole genome sequences of these four viruses were obtained.The complete genome sequences of four viruses were obtained by sequencing and splicing. 【Result and conclusion】 Analyses showed that the full length of these four viruses was 10 990 bp, no Ploy (A) tail structure comprising one large ORF, encoding 3 426 amino acids. The 5′ non-coding region (5′UTR) contained 94 bp. Ten bases were missing from 103 395 bp to 103 411 bp of GDNS2010.1 and GDNS2010.2 strains in the 3′ non-coding region (3′UTR). Two sequences of GDHZ2012.1 and GDHZ2012.2 preliminarily determined were joined for a sequence analysis. DNAstar and MEGA6.0 were used to analyze the sequences of six virus strains. Comparisons with other domestic Tembusu viruses recorded in GenBank showed that the similarity of the nucleic acid sequence was more than 98%. In comparison with Ntaya virus, Sitiawan virus, the similarity was about 73%. Compared with West Nile virus, Japanese encephalitis virus and yellow fever virus, the similarities were less than 63%. The similarity for nucleic acid sequence of envelope protein in the six isolates remained between 97.5%-99.9%; the similarity of deduced amino acid sequence was found to be more than 97% whereas isolates from the same area had 99.9% similarity. In the site of E154 in envelope, there are a potential glycosylation site Asn-Try-Ser and a potential virulence loci in E289.