The objective of this study is to develop a rapid and accurate multigene phylogenetic analysis to identify Potato virus Y (PVY) strains. The phylogenetic relationships of strains within the PVY species were evaluated with isolate-strain association using five datasets of concatenated sequences from the P1, HC-pro, VPg and CP genes to determine the best dataset for PVY strain identification. Results from phylogenetic analyses and Bayesian tip-association significance (BaTS) tests indicated that the major PVY strains could be distinguished using the P1, VPg and CP concatenated sequences datasets but not the remaining concatenated sequence datasets. Phylogenetic trees reconstructed from the concatenated sequences of P1, VPg and CP genes revealed that the ML and NJ trees had broadly similar topologies and that both were better than the maximum clade credibility tree (MCC). Additionally, the full genome of HLJ26, one isolate randomly selected for the multigene phylogenetic analysis, was clustered with high confidence among members of the PVYNTN-NW (SYR-Ⅱ) strain, which includes isolates of SYR-Ⅱ-2-8, SYR-Ⅱ-Be1 and SYR-Ⅱ-DrH. This suggests that it was a PVYNTN-NW (SYR-Ⅱ) isolate. Recombination analysis of this isolate identified four putative recombination joints in the P1, HC-pro/P3, VPg and the 5'-terminus of CP. This pattern is similar to that observed in the genomic structure of PVYNTN-NW (SYR-I), supporting the classification of this isolate as the PVYNTN-NW strain (SYR-Ⅱ). Simultaneously, two expected fragments of approximately 1 000 and 400 bp in size were also amplified from the isolate by a multiplex RT-PCR, consistent with the expected band pattern of the PVYNTN-NW (SYR-Ⅱ) strain. This further supports the utility of the multigene phylogenetic method in identifying PVY strains. We propose that the major PVY strains could be distinguished accurately using multigene phylogenetic analysis based on the concatenated sequences from the P1, VPg and CP genes.