Varying effectiveness of metalaxyl fungicides and disease incidences caused by downy mildew to maize in several places in Indonesia led to the speculation that genetic variation of Peronosclerospora species in Indonesia exists. Hence, we employed two molecular marker systems, namely SSR (Simple Sequence Repeat) and ARDRA (Amplified Ribosomal DNA Restriction Analysis) markers, to study the population structure and genetic diversity of downy mildew isolates collected from hotspot production areas of maize in Indonesia. Both molecular techniques grouped the isolates into three clusters with a genetic similarity between 66-98% and 58-100% for SSR and ARDRA markers, respectively. In general, SSRs yielded lower similarities among isolates compared to ARDRA. Combined analysis of data from both techniques resulted in genetic similarities of 64-98% for 31 downy mildew isolates grouped into three clusters, two clusters of Java, and one cluster of Lampung and Gorontalo isolates. This study demonstrates a close relationship between geographical location and genetic similarity of downy mildew isolates. High levels of diversity of Peronosclerospora spp. in Java could be due to two causes, due to genetic variation within P. maydis, or due to presence of further mildew species besides P. maydis in Java, which are able to infect maize. Results obtained from this research provides a good explanation for frequent breakdown of resistance in downy mildew-resistant cultivars and is essential for devising more effective strategies to reduce the impact of downy mildew in maize.