Downy mildew (Peronosclerospora maydis) is considered one of the most destructive diseases for maize. Beside being dispersed by air, it is suspected that contaminated seeds also play a role in the dissemination of this disease. To answer this hypothesis we collected sweet corn and field corn samples from three districts in East Java province, Indonesia. A number of representative infected and healthy looking ears were collected from those regions. Twenty seeds were randomly taken from each cob. DNA derived from twenty seeds was pooled and genotyped with multiplexing using maize microsatellite (bnlg1189) and downy mildew microsatellite (DM38) primer. Allele in the size of 153bp can be observed after the infected samples were amplified with DM38, while the size of the maize microsatellite allele depends on the genotype of infected maize. All seeds collected from infected ears positively carry the DM allele. Meanwhile, our genotyping data revealed that 30-80% of healthy sweet corn ears positively contained the DM allele, while only 8.3 % of healthy field corn ears contained the DM allele. Specificity of the primers was verified by the absence of cross-reaction with DNA from 6 common contaminants on maize seeds, while sensitivity tests indicated that 10 pg is the threshold for the detection of Peronosclerospora maydis. The results obtained from this study implicate contaminated seeds as possible sources of initial inoculums of maize downy mildew in the field and also provided a simple and accurate diagnostic method to assess the presence of downy mildew in maize seeds.