Manchu forces broke through Shanhai Pass in 1644 and rapidly overwhelmed the Ming Dynasty. In 1661, a naval fleet led by the Ming loyalist Koxinga, arrived in Taiwan to oust the Dutch from Zeelandia and establish a pro-Ming base in Taiwan (Spence 1999:46-49).

Koxinga was born to Zheng Zhilong, a Chinese merchant and pirate, and Tagawa Matsu, a Japanese woman, in 1624 in Hirado, Nagasaki Prefecture, Japan. He was raised there until seven and moved to Quanzhou, in the Fujian province of China. In a family made wealthy from shipping and piracy, Koxinga inherited his father's trade networks, which stretched from Nagasaki to Macao. Following the Manchu advance on Fujian, Koxinga retreated from his stronghold in Amoy (Xiamen) and besieged Taiwan in the hope of establishing a strategic base to marshal his troops to retake his base at Amoy. In 1662, following a nine month siege, Koxinga captured the Dutch fortress Zeelandia and Taiwan became his base (see Kingdom of Tungning) (Clements 2004:188-201). Concurrently the last Ming pretender had been captured and killed by General Wu Sangui, extinguishing any hope Koxinga may have had of re-establishing the Ming Empire. He died four months thereafter in a fit of madness after learning of the cruel killings of his father and brother at the hands of the Manchus. Other accounts are more simple, attributing Koxinga's death to a case of malaria (Spence 1999:51-57; Clements 2003:215).

Naval and troop forces of Southern Fujian defeated the Dutch in 1662, subsequently expelling the Dutch government and military from the island. They were led by Koxinga (鄭成功). Following the fall of the Ming Dynasty, Koxinga retreated to Taiwan as a self-styled Ming loyalist and established the Kingdom of Tungning (1662–83). Koxinga established his capital at Tainan and he and his heirs, Zheng Jing (鄭經), who ruled from 1662–82, and Zheng Keshuang (鄭克塽), who served less than a year, continued to launch raids on the south-east coast of mainland China well into the Qing Dynasty, attempting to recover the mainland.

In 1683, following the defeat of Koxinga's grandson by an armada led by Admiral Shi Lang of Southern Fujian, the Qing Dynasty formally annexed Taiwan, placing it under the jurisdiction of Fujian province. The Qing Dynasty government tried to reduce piracy and vagrancy in the area, issuing a series of edicts to manage immigration and respect aboriginal land rights. Immigrants mostly from Southern Fujian continued to enter Taiwan. The border between taxpaying lands and "savage" lands shifted eastward, with some aborigines 'Sinicizing' while others retreated into the mountains. During this time, there were a number of conflicts between Chinese from different regions of Southern Fujian, and between Southern Fujian Chinese and aborigines.

In 1887, the Qing government upgraded Taiwan's status from prefecture of Fujian to full province, the twentieth in the country, with its capital at Taipei. This was accompanied by a modernization drive that included building Taiwan's first railroad and starting a postal service

Reference

http://en.wikipedia.org/wiki/History_of_Taiwan