Viral diseases of the sweet potato (Ipomoea batatas L. (Lam)) are highly prevalent and often cause serious damage to the plants, particularly the severe strain of the sweet potato feathery mottle virus (SPFMV-S) that causes ‘obizyo-sohi’ disease in Japan. To confer viral resistance to SPFMV using current biotechnology, a transgenic sweet potato has been developed by introducing SPFMV-S coat protein (CP) genes, which have shown significant resistance to SPFMV-S; however, ecological distribution in the field of SPFMVs is unclear. This study investigated the ecological distribution of SPFMVs in field-infected sweet potato, and virus resistance nearer to the field was evaluated in transgenic sweet potato. SPFMV was not capable of independent infection; rather, infection by SPFMVs was coincidentally complex under natural conditions. Furthermore, infection was by a dominant strain between complex infecting SPFMVs, and was differentiated by the area of infection. Transgenic sweet potato plants expressing the SPFMV-S CP gene were challenged by graft inoculation with field-infected SPFMVs. All of the transgenic sweet potato plants were highly protected in the long term against SPFMV complex infection compared to control plants. These results suggest that transgenic sweet potato can acquire resistance to SPFMVs in the field.