From: http://www.colorq.org/MeltingPot/article.aspx?d=Asia&x=MalayChinese

Chinese/Native intermarriage in Taiwan
The earliest instances of Austronesian and Chinese intermarriage
probably occured on the island of Taiwan. Prior to Chinese
immigration, the inhabitants of of Taiwan were the descendants of
neolithic Austronesians who settled the island around 4000 B.C.,
absorbing the previous inhabitants.1 Immigrants from China started
entering Taiwan as early as the 7th century A.D.2 Significant numbers
of Hakka from China had established themselves in Taiwan by the 10th
century, they were followed by migrants from Fujian Province, across
the strait from Taiwan.3. But large scale Chinese immigration did not
take place until European powers established their rule on the island
in the 16th-17th century.4 The Dutch in particular encouraged Chinese
immigration as a source of agricultural labor for cash crops.5 Chinese
immigration continued after Koxinga's forces from China took control
of Taiwan in 1644.6

Most of the early Chinese immigrants were male, and marriages with
aboriginal women was common.7 There was an old saying among Taiwanese
Chinese: 'We have China fathers but not China mothers.' The pingpu,
inhabitants of the western plains, were the first aborigines to
encounter Chinese migrants; their intermarriage with the Chinese and
the adaptation of Chinese names was documented during the Qing
Dynasty.8 Pingpu intermarriage with Chinese and assimilation into
Chinese culture occured to such a degree that the pingpu's Aborigine
status has come under dispute in modern times.9

Although 98% of Taiwan's population today is officially classified as
Han Chinese, while the remaining 2% are classified as aborigines, the
percentage of Taiwanese 'Chinese' with aborigine ancestry is quite
high. Among the benshengren (Chinese Taiwanese descended from Chinese
immigrants who arrived before the KMT takeover) population, recent
genetic studies reveal that more than 88% of the benshengren
population have some degree of aboriginal heritage.10

Chinese/Native intermarriage in Malaysia/Indonesia
Chinese junks first started visiting the Malay world around the 9th
century. As early as the 10th century, Chinese refugees from Guangdong
and Fujian settled in Java. There had been small numbers of Chinese
present in Malaysia and Indonesia prior to the 15th century, but large
scale immigrations took place after the reopening of trade routes
between China and the Malay world following the visits of the Chinese
envoy Zheng He. Another wave of Chinese came to the Philippines during
the 16th century to seek opportunities in the Spanish-controlled
Mexico-Manila trade, boosting Manila's Chinese population
dramatically.11 During the 19th century, the coolie trade brought
another influx of Chinese immigrants to the region. Many worked the
plantations of European masters in Malaysia and Indonesia.

Chinese Muslims integrated easily into Muslim communities in
pre-dominantly Islamic Malaysia and Indonesia, marrying local Muslims.
Their children identified as Malay or members of other indigenous
ethnic groups. Some of these Chinese immigrants were already Muslims
in China. The current Prime Minister of Malaysia is the descendant of
a Muslim man from China and a local woman. Prime Minister Abdullah
Ahmad Badawi's maternal grandfather Hassan (Ha Su Chiang) came from
China's Hainan Island to Malaya in the mid 19th century.12 Badawi's
Chinese relatives lived in the Muslim village of Hainan's Sanya city,
home to descendants of Muslim immigrants from Arabia, Persia and
Vietnam who came to China to trade.13 (For more information on the
history of Muslims in China, see West Asians in China.)

Other Chinese converted to Islam during their sojourn in Malaya or
Indonesia. In parts of Indonesia, Chinese closely involved with native
courts tended to convert to Islam and marry native women.14

The Peranakan Chinese of Indonesia/Malaysia/Singapore
Non-Muslim Chinese also intermarried with local women. Chinese
immigrant fathers often preferred that their mixed children be
identified as Chinese, and married their daughters to other Chinese.15
Those who had become well-off could also acquire brides from China for
their sons. A new cultural group, distinct from either the natives or
the 'full-blooded' Chinese, came into being. They came to be known as
the Peranakan Chinese. (The term 'Peranakan' itself encompasses other
immigrant groups, such as Indians, which adopted a native lifestyle.)
The Chinese Peranakan men are called Baba and traditionally wear
Chinese apparel. The women are called Nonya and combine Malay dress
styles with Chinese influences. The blending of cultures is also
reflected in the famed Nonya cuisine.

Most Peranakan communities speak native languages as the home language
(albeit with many Chinese dialect loan words). Others speak Chinese
dialects. Most retain ancestral Chinese religions or accept
Christianity.

Relations between Peranakan Chinese and "full-blooded" Chinese
In Singapore, full-blooded Chinese regard the Peranakan as a more
beautiful people because of large eyes and distinct features inherited
from Malay foremothers. In the past, many older Peranakan regarded
more recent immigrants from China as unintegrated foreigners who did
not fit into local life. Some full-blooded Chinese in turn mocked the
Peranakan as "Chinese who are not Chinese". Today, the line between
Peranakan and full-blooded Chinese is blurring due to a high level of
intermarriage between the 2 communities, and the government policy
that the Chinese language should be taught to all Chinese children,
whether they are of Peranakan or "new immigrant" background.

In Indonesia, the more recent, 'pure-blooded' ethnic Chinese tend to
look down on the Peranakan Chinese. Documented history give many
illustrations: In Jakarta in the 50s-70s, the Glodok complex was owned
only by Encek-encek's, the slang word for pure bred ethnic Chinese.
Peranakans were (and still are) seen to be of lower class and thus not
worthy of setting shop there.

The Peranakans themselves sometimes look unfavorably upon the recent
immigrants because they feel that the recent immigrants' lack of
integration fuels negative perceptions against all ethnic Chinese.
These fears proved well-founded in the light of in recent tensions
between the ethnic Chinese and the native Indonesians, in which both
Peranakan and full-blooded Chinese were targeted for violence.

The Chinese mestizos of the Philippines
A distinct mixed Chinese-indigenous cultural group arose in the
Philippines, as it did in Malaysia and Indonesia. The early Chinese
immigrants were mostly men. Many took native wives. By the 19th
century, the mixed descendants of Chinese men and Filipinas had
established themselves as a community separate from the Chinese. They
were called Mestizo de Sangley (A mestizo is someone of mixed
parentage, while Sangley, from Hokkien seng di, meaning to trade, was
the generic name of the Chinese as used by the Spaniards here in the
Philippines.16

In the 20th century, the Chinese-Filipino mestizos have lost their
identity as a distinct communities as new mestizos came to be counted
as either Chinese or native Filipino.17 A large proportion of
Filipinos, especially those from areas with a high mercantile
population, have Chinese ancestry, but they no longer identify as
Chinese mestizos.

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More planned to come...