Chinese foxglove and glutinous rehmannia are major cultivated lines of Rehmannia glutinosa (Gaertn.) Libosch. ex Fisch. et C.A.Mey., which belongs to the family Rehmanniaceae, and their roots are widely used with other medicinal herbs as traditional natural medicine. These plants are grown by vegetative propagation; therefore, once plant pathogenic viruses infect to these plants, the pathogens remain in the plant and affect root quality and yield. Since identification of pathogenic viruses in the plants is fundamental to controlling viral diseases, we used a bioassay and next-generation sequencing (NGS) to investigate plant viruses infecting Chinese foxglove and glutinous rehmannia in Toyama Prefecture in Japan. Broad bean wilt virus 2 (BBWV2) and Cucumber mosaic virus were detected with NGS and isolated by bioassay from Chinese foxglove. Several contigs of nucleotide sequences of six plant viruses such as Amazon lily mild mottle virus (ALiMMV), BBWV2, Citrus leaf blotch virus (CLBV), Cnidium vein yellowing virus (CVYV), Plantago asiatica mosaic virus (PlAMV) and Youcai mosaic virus (YoMV) were detected with NGS from glutinous rehmannia. Of these, BBWV2, PlAMV and YoMV were successfully isolated by bioassay, and partial genome sequences of ALiMMV, CLBV and CVYV were detected by RT-PCR. Back inoculation of virus-free host plants with the individual isolated viruses showed that infected Chinese foxglove exhibited mild yellowing and mosaic symptoms, but glutinous rehmannia did not have any symptoms in single viral infection. These results suggest that in fields, latent infections of glutinous rehmannia with these viruses should be considered important for controlling secondary infection of any neighboring or rotation crops. This report is the first of BBWV2, PlAMV and YoMV as causal agents of viral diseases in Chinese foxglove and glutinous rehmannia in Japan.