Kemudian, pedagang [[Islam di Tiongkok|Tionghoa Muslim]] dari pesisir timur Tiongkok tiba di kota-kota pesisir Indonesia dan [[Malaysia]] pada awal abad ke-15. Mereka dipimpin oleh marinir [[Zheng He]], yang memimpin [[Pelayaran Cheng Ho ke Samudra Barat|beberapa ekspedisi ke Asia tenggara]] antara tahun 1405 dan 1430.{{sfn|Ma|2005|p=115}} Para pedagang ini menetap di pesisir utara [[Jawa]], tetapi tidak ada dokumentasi lebih lanjut mengenai pemukiman mereka setelah abad ke-16. Para sarjana meyakini bahwa orang-orang Tionghoa Muslim ini diserap ke dalam populasi Muslim mayoritas,{{sfn|Tan|2005|p=795}} hingga tidak ada komunitas Tionghoa tersisa ketika Belanda tiba.{{sfn|Reid|2001|p=33}} Perdagangan dari Tiongkok ditetapkan kebali ketika Tiongkok mengesahkan perdagangan swasta pada tahun 1567 dan mulai memberi izin 50 [[kapal jung]] dalam satu tahun. Koloni-koloni Tionghoa yang berbeda muncul di pelabuhan-pelabuhan di seluruh Nusantara, termasuk pelabuhan lada di [[Banten]].{{sfn|Reid|1999|p=52}}
=== ColonialEra erakolonial ===
[[File:Tableau de la Partie de Batavia, ou s'est fait proprement le terrible Massacre des Chinois, le 9 Octob.jpeg|thumb|Chinese-owned houses were burned, while bodies were dumped into rivers and canals]]
ByHingga tahun 1740, theretelah wereada overlebih dari 2,.500 Chinese-ownedrumah housesyang withindimiliki theorang Tionghoa di dalam tembok kota [[Batavia, DutchHindia East IndiesBelanda|Batavia]] city walls, with anotherdengan 15,000 individualsindividu livinglainnya outsidetinggal ofdi theluar citybatas limitskota.{{sfn|Setiono|2008|p=109}} The Dutch colonials required them to carry registration papers, and those who did not comply were deported to China. After an outbreak of [[malaria]] killed thousands in the 1730s, including the [[List of Governors-General of the Dutch East Indies|Governor-General of the Dutch East Indies]], [[Dirck van Cloon]], the deportation policy was tightened.{{sfn|Setiono|2008|pp=111–113}} According to Indonesian historian [[Benny G. Setiono]], the outbreak was followed by increased suspicion and resentment in native Indonesians and the Dutch toward the ethnic Chinese, who were growing in number and whose wealth was increasingly visible.{{sfn|Setiono|2008|pp=111–113}} As a result, Commissioner of Native Affairs Roy Ferdinand, under orders of Governor-General [[Adriaan Valckenier]], decreed on 25 July 1740 that Chinese considered suspicious would be deported to [[Dutch Ceylon|Ceylon]] (modern day Sri Lanka) to harvest cinnamon.{{sfn|Setiono|2008|pp=111–113}} Wealthy Chinese were extorted by corrupt Dutch officials who threatened them with deportation;{{sfn|Setiono|2008|pp=111–113}} There were also rumours that deportees were not taken to their destinations but were thrown overboard once out of sight of Java, and in some accounts, they died when rioting on the ships.<ref name=raffles/>
