Sugarcane mosaic virus (SCMV) is one of the devastating virus diseases of maize in the world. Understanding the genetic of resistance gene(s) is the basis for effective selection in resistance breeding program. In this study, analyses were conducted to determine the genetic basis in line Siyi with tropic germplasm conferring complete resistance to SCMV. Based on the responses of parents and F-1, F-2 and backcross populations in three successive years' field trails, two dominant complementary genes, were found to condition the resistance by Mendelian genetic analysis. The two genes were mapped on chromosome 3 and chromosome 6, respectively using microsatellite markers. The resistance gene on chromosome 3 (bin 3.04/05) was flanked by simple sequence repeal: markers umc1527 and phi053 with the genetic distances of 1.8 and 2.1 cM, respectively; whereas the genetic distances between the two flanking markers umc2311 and bnlg1371 and resistance gene on chromosome 6 (bin 6.00/01) was 2.1 and 1.5 cM, respectively. Genotypic analysis of the plants from backcross and F-3 populations also validated the two genes with the unique genetic model. For further confirming the interaction between the two genes, a set of near isogenic lines (NILs) carrying different number of the resistance genes were developed, genotypic analysis of NILs clearly show that two dominant complementary genes cooperatively control the resistance to SCMV in maize.