According to the sequence from the electronic cloning, a pair of primers were designed to clone the Arf6 gene in Litopenaeus vannamei by PCR. A 695bp cDNA was obtained, which contained a 96bp 5′ untranslated region (UTR), a 528bp open reading frame (ORF), and a 71bp 3′ UTR. The encoded protein was composed of 175 amino acids, with a molecular weight of 20kDa and the calculated isoelectric point of 8.82. The molecular formula was predicted to be C896 H1426 N252 O255 S8. The deduced amino acid sequence showed that the protein encoded by the Arf6 gene owned a conserved GTP-binding domain, 21 negatively charged residues (Asp+Glu) and 25 positively charged residues (Arg Lys). The obtained sequence was compared with the other species through BLAST analysis, indicating that the amino acid sequence cloned in this study is highly conserved. Phylogenetic analysis based on the amino acid sequences revealed that L. vannamei is closely related to Drosophila melanogaster. Semi-quantitative RT-PCR results showed that the gene was expressed in most of the examined tissues, and the highest expression level was observed in the hepatopancreas, while the lowest in the eyestalk. Arf6 gene expression level in the hepatopancreas of L. vanname that was infected by the taura syndrome virus (TSV) was higher than that of the specific pathogen free L. vanname. The protein functional classification results suggested that the Arf6 plays a potential role in the pathogen host defense systems as an immune response factor.