In yellow soybeans, inhibition of seed coat pigmentation by RNA silencing of CHS genes is suppressed by low temperature and a viral suppressor, resulting in ‘cold-induced seed coat discoloration’ and ‘seed mottling’, respectively. Differences exist in the degree of cold-induced seed coat discoloration among Japanese yellow soybean cultivars; for example, Toyomusume is sensitive, Toyohomare has some tolerance, and Toyoharuka is highly tolerant. In this study, we compared the degree of seed mottling severity due to soybean mosaic virus (SMV) among these three soybean cultivars. Obvious differences were found, with the order of severity as follows: Toyohomare > Toyomusume > Toyoharuka. RNA gel blot analysis indicated that CHS transcript abundance in the seed coat, which was increased by SMV infection, was responsible for the severity of seed mottling. Quantitative reverse transcription PCR analysis revealed why mottling was most severe in SMV-infected Toyohomare: the SMV titer in its seed coat was higher than in the other two infected cultivars. We further suggest that a major gene ( Ic ) for tolerance to cold-induced seed coat discoloration can relieve the severity of seed mottling in SMV-infected Toyoharuka.