An avian influenza virus strain, A/domestic green-winged teal/Hunan/2036/2007(H3N6) (DGW-T2036), was isolated from healthy domestic green-winged teals (Anas crecca) in Hunan Province, South China. All eight gene segments of the isolate were sequenced. Genomic analysis demonstrated that this H3N6 virus is a novel reassortant avian influenza virus with a gene constellation originating from multiple ancestors.