Satsuma dwarf virus (SDV) and its strains including citrus mosaic virus (CiMV), navel orange infectious mottling virus (NIMV), Natsusdaidai dwarf virus (NDV), and Hyuganatsu virus (HV), are known to cause severe damages to citrus trees. The occurrence of SDV strains was investigated in 69 citrus orchards in Mie Prefecture, Japan, in 2010–2012. Forty-three of the orchards contained citrus trees infected with strains of SDV. The CiMV strain occurred most frequently in Mie Prefecture, followed by the SDV strain. An isolate of the NIMV strain was detected at two orchards in Mie Prefecture. This is the second occurrence of NIMV in a field outside of the original field in Wakayama Prefecture, following an occurrence in Ehime Prefecture. This is the first report of combined CiMV and NIMV infection of citrus. Our results reveal that the CiMV strain is widely distributed outside Wakayama Prefecture. Moreover, isolates of the CiMV strain that barely induce mosaic symptoms on the fruit rind were found to be widely distributed. Because CiMV causes milder foliar symptoms than does SDV, it is considered that milder CiMV isolates are widespread in Mie Prefecture. Trifoliate orange seedlings were planted near infected citrus trees growing on trifoliate orange rootstocks, and soil-transmission of the SDV and CiMV strains occurred within 1 year of planting. Because trifoliate orange is widely used as a citrus rootstock, similar infections may occur in citrus plants grafted onto this rootstock in fields containing infected citrus trees.