The genetic diversity and phylogenetic relationships of Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus G (SPVG), two major sweet potato viruses in Sichuan, the largest sweet potato producing area of China, were analyzed. A total of 18 virus isolates, including 12 SPFMV isolates and six SPVG isolates, were obtained from different fields and characterized by RT-PCR and sequencing. Sequence alignments revealed 77.3%-99.8% and 85.4%-99.6% nucleotide identities for the coat protein gene of SPFMV and SPVG, respectively. Phylogenetic analysis divided SPFMV isolates into groups RC, O and C, and SPGV isolates into groups CH and CH2. The information presented in this study is useful for the development of engineered resistance to local virus strains in sweet potato.