The complete sequence of GF_YL20, a potato virus Y (PVY) isolate from China, encodes a polyprotein of 3,061 amino acids. Sequence analysis indicates that GF_YL20 has a genomic structure different from previously reported PVY strains. It shares 99 % nucleotide sequence identity with PB209 (PVY(N:O)) except in VPg, but more than 97 % nucleotide sequence identity with the VPg of Mont (PVY(N)), PB312 (PVY(NTN)) and HN2 (SYR-I). Phylogenetic analysis indicates that GF_YL20 is a novel N:O recombinant with three recombination breakpoints.