To investigate the composition and distribution of Potato virus Y (PVY) strains across different hosts in China, phylogenetic and recombination analyses were studied using 31 complete coding sequences in PVY isolates from China. Phylogenetic analysis revealed that the NJ and ML bootstrap trees had broadly similar topologies, in which 6 isolates of GF_YL20, FZ10, DF, SD1, 1116 and 9703-3 are divergent from all known PVY strains and the remaining isolates from the same strain tended to group together with high bootstrap supports, showing a distinct strain feature among PVY isolates. Significant recombination signals were identified in 28 out of the 31 PVY isolates and the majority of them classified to PVY^N-Wi, PVY^NTN and PVY^NTN-NW. Further analysis showed that 5 isolates of 1104, DF, SD1, 1116 and 9703-3 are novel N×O recombinants. Results from the composition and distribution of PVY strains indicated that recombinant strains were dominant in the PYV isolates in China, thus, it is important to monitor the development of these recombinants in the practice. The above results showed that all PVY isolates could be distinguished accurately using phylogenetic combine with recombination analyses.