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When the Kangxi Emperor entrusted the Jesuit missionaries with the cartographical survey of his empire, the provinces of Henan, Zhejiang, and Fujian, and the Island of Formosa, fell to the lot of Mailla along with Jean-Baptiste Régis and Roman Hinderer.
In this period the US navy was also steamed into the Formosa Straits as a deterrent to prevent conflict between the Chinese nationalists who had escaped to the island of Formosa and the Chinese communists in mainland China.
In June 1897, he was appointed by President Cleveland consular agent for the island of Formosa, where he remained nine years, during which time he wrote numerous monographs on Formosan affairs.