Western Eurasia, notably the Near East and South Asia (Indian sub-continent), has interacted with Indonesia through Indian Ocean trade (the Maritime Silk Route) for more than 2000 years. The Indianization, and later Islamization, of Indonesia was enacted largely through trading activities, but also spread with help from the many Indianized and Islamic kingdoms that reigned over parts of the Indonesian archipelago during this time. Western Eurasian interaction left behind not only imported trade goods and cultural features, but also genetic traces. To locate the primary areas of Western Eurasian genetic influence in Indonesia, we have assembled published uniparental genetic data from ∼2900 Indonesian individuals. Frequency distributions show that Western Eurasian paternal lineages are found more commonly than Western Eurasian maternal lineages. Furthermore, the origins of these paternal lineages are more diverse than the corresponding maternal lineages, predominantly tracing back to South West and South Asia, and the Indian sub-continent, respectively. Indianized kingdoms in the Indonesian archipelago likely played a major role in dispersing Western Eurasian lineages, as these kingdoms overlap geographically with the current distribution of individuals carrying Western Eurasian genetic markers. Our data highlight the important role of these Western Eurasian migrants in contributing to the complexity of genetic diversity across the Indonesian archipelago today.