Maize dwarf mosaic virus caused by Sugarcane mosaic virus (SCMV) is one of the important diseases in maize growing area in Huanghuaihai Area of China, and development of effective markers associated with SCMV resistance is the basis of marker-assisted selection (MAS). In this study, conserved domains of disease-resistant genes were investigated within the consensus SCMV-resistance QTL on the maize bin 6.00-6.01, and furthermore the polymorphic sequences were used to develop markers InDel-130 and InDel-110. As a result, InDel-110 that was significantly associated with SCMV resistance was validated by the χ2 independence test of the number of resistant and susceptible marker genotypes in 102 inbred lines, and could be used for MAS for sugarcane mosaic virus resistance in maize.