The nations of the Indonesian Archipelago - the Republics of Indonesia and Malaysia, and the Sultanate of Brunei - are cultural and linguistic diverse, but in some ways historically uniform. Long before the beginning of the study period, these islands had been settled by speakers of Austronesian languages that probably originated on Taiwan. Their cutures were united in possessing agriculture and a competent maritime technology with which they traded among one another and with neighboring countries. Indeed, by CE 1 Malayo-indonesian mariners had established trading contact with East Africa and may have already begun settling Madagascar. Thus, If your ancestors were in the Indonesian Archipelago in CE 500, their ancestors were probably also there in CE 1 - probably on the same island. Note the inevitable effect of maritiem commerce, however, a gradual diffusion of genes to neighboring islands or adjacent lands.
The region's geography - a vast archipelago of mountainous volcanic islands straddling the sea routes between Asia's two great cultural centers, India and China determined that for most of their history:
Sixth century - The arrival of Hinduism: During the sixth century, Indonesia was contacted by Hindu missionaries, and the faith quickly spread throughout the islands. Certainly these Indians contributed their genes to the population, so if your ancestors were in the Indonesian Archipelago in CE 1000, their ancestors might also have been in India (probably eastern) in CE 500.
Thirteenth Century - The arrival of Islam: Indonesian Hinduism evolved into a philosophy supporting the divine authority of the regions many kings, who used their authority to promote and monopolize foreign trade by requiring farmers to pay taxes in kind of export goods such as spices. When Muslim traders (from India, again) arrived in Western Sumatra (modern Aceh) at the end of the thirteenth century, Islam's egalitarian message was highly appealing and the religion spread quickly throughout the islands. Thus, although Islam spread quickly, the genetic imprint of the non-Indonesian Muslims who introduced it is mostly limited to Sumatra. Nevertheless, if you had ancestors in western Sumatra in CE 1490, they might have had ancestors both there and in eastern India (probably Bengal State and Bangladesh) in CE 1000. (For all its revolutionary potential, Indonesian Islam never succeeded in undermining the prerogatives of kings.)
Seventeenth Century - The Dutch: During the sixteenth century, European powers discivered the Indonesian Archipelago's wealth of argicultural and forest products. By 1600, Dutch traders, organized under the Dutch East India Company had driven out European competitors such as the Portuguese and monopolized Indonesian trade with the West, establishing their main outpost of Batavia (modern Jakarta) on Java home of Indonesia's most powerful and prestigious kingdoms. As trade monopolists, the Dutch fit in nicely with local concepts of politics, and gradually coopted local rulers, whose monopolies on fireign trade they took over. Through the eighteenth centuries, they were largely restricted to Java. So, if your ancestors were on Java in CE 1800, it is possible that some of their ancestors were in the Netherlands in CE 1490. Look to family folklore and the evidence of your senses.
Nineteenth Century - The Dutch take over: At this point, the Dutch expanded their control from Java to the entire archipelago. So, if your ancestors were anywhere in the Indonesian Archipelago in CE 1900, it is possible that some of their ancestors were in the Netherlands or in the Dutch colonies of Java in CE 1800. Look to family folklore and the evidence of your senses.
Twentieth Century - A Japanese interlude: For over three years during WWII, Japan ruled the Indonesian Archipelago as a colony. They gave the Dutch the boot, replacing Dutch administrators with with native Indonesians in an arrangement that ranged from hostile to almost friendly. If you have recent Japanese ancestry, your family folklore should fill you in.