Around 4000 years ago, there was notable gene flow from India into Australia, though the extact circumstances surrounding this event aren't yet understood, though it may be tied up in the same event that brought the dingo to Australia.

Off the coast of Arnhem Land, in the far north of Australia, a 12th Century coin from the Kilwa Sultanate was discovered. It's uncertain whether it arrived there as part of the Indian Ocean trade network that connected Kilwa to ports in eastern Asia or whether it arrived much later, with the Portuguese.

Also in this area of Australia we have oral history concerning the Baijini, who encountered the Djanggawul Ancestors of the Yolngu. The Baijini came down from the north to harvest trepang (sea cucumbers used in Chinese cuisine) and introduced the tamarind tree to the area. Both are traits associated with the historic Macassan trepangers from Sulawesi, but the Baijini are explicitly said to have pre-dated the Macassans and are regarded as a distinct people by the Yolngu.

As for the Macassans, there's considerable debate concerning when they started sailing to Arnhem Land and the Kimberley. Certainly they were active in the area by the 1700s, but how much earlier than that? Rock art depicting Macassan praus have been dated to at least 1664, and possibly as early as 1517. Some old trepanger camps have been dated to between 1170 and 1520, though those dates have been questioned, with the oldest occupation at these sites being interpreted as purely Aboriginal rather than having an Indonesian component.