The complete sequence of CF_YL21, a Potato virus Y (PVY) isolate from Solanum tuberosum in China, was determined to be 9718 nucleotides in length, excluding the 3′-terminal poly(A) tail. The viral genome had a single open reading frame of 9186 nucleotides encoding a polyprotein of 3061 amino acids. The polyprotein was predicted to be cleaved into ten functional proteins by three viral proteases. Sequence analyses indicated that CF_YL21 shared 97% nucleotide identity with Wilga5 (PVYN-Wi), and two putative recombination signals were detected in the P1 and HC-Pro/P3 regions. Phylogenetic analyses, Bayesian Tip-association Significance (BaTS) test, and multiplex RT-PCR assay confirmed that the isolate had the similar molecular and genomic structure with PVYN-Wi, a PVY strain formed by recombination between PVYN and PVYO. To our knowledge, this is the first report of the complete sequence structure of PVYN-Wi strain from potato in China.